NAIROBI, Kenya — The United States ambassador to Kenya was frustrated. It was almost eight months after suicide bombers blew up part of a resort hotel at almost exactly the same time other terrorists tried to shoot down an Israeli airliner taking off from nearby Mombasa-Moi International Airport — yet no one had been convicted.

“There are Kenyan citizens who have and continue to put outside interests and ideologies ahead of the welfare and well-being of Kenya,” Johnnie Carson, the ambassador at the time, said pointedly after a ceremony. He repeated the complaint the next day in an interview with a Nairobi television station.

The three countries — Kenya, Tanzania and Uganda, whose human rights records have long been described as “poor” or ones with “serious problems” by the U.S. State Department — have received millions in U.S. aid since the September 11, 2001, attacks on the World Trade Center and the Pentagon. And the U.S. has pushed the countries to enact anti-terrorism laws that critics say lack protection for civil liberties.Suddenly, what had been a low-key ordeal for Kubwa Mohammed Seif and his father, who had been arrested for suspected involvement in the 2002 resort attacks and who had later been released, turned into an oppressive experience that led to their being tried for murder. Their story became Exhibit A for human rights advocates who say U.S. anti-terrorism dollars and political pressure are encouraging three East African countries known for human rights failings to be even more repressive.

Growing anti-American animosity in East Africa reflects a broader challenge that the United States faces around the world: how to take effective steps against terrorism without alienating the very people the U.S. says it wants to help.

No anti-terrorism laws until after 9/11

That terrorism in the region should be a concern is little wonder. In 1998, al Qaeda attackers executed twin bombings of the U.S. embassies in Nairobi, Kenya’s capital, and Dar es Salaam, Tanzania’s biggest city. The Nairobi attack killed 201 Kenyans and 12 Americans; more than 4,000 were injured. In Dar es Salaam, the bomber never reached his intended target but still killed 12 people and wounded 85.

Then, in the heightened tension a year after 9/11, terrorists fired two shoulder-launched missiles at an Israeli airliner taking off from the coastal Kenyan city of Mombasa. They missed, but minutes later, car bombers blew up the Paradise Hotel, an Indian Ocean beach resort in nearby Kikambala that’s favored by Israeli tourists. The blast killed 10 Kenyans and three Israelis; 80 were injured.

Despite the 1998 attacks, neither Kenya nor Uganda or Tanzania took steps to pass legislation to deal with terrorism. Until 9/11, said Paul Kibugi Muite, a member of Kenya’s Parliament and chairman of the parliamentary Committee for Justice and Legal Affairs, many East Africans believed that terrorism was aimed at foreigners — Americans and, later, Israelis. In an interview with the International Consortium of Investigative Journalists, he characterized the attitude as, “We’re not the problem — the Americans are. This is their fight.” The view, he said, was that the U.S. should compensate other countries for what he called collateral damage.

But then the U.S. started encouraging and cajoling countries all over the world to join its efforts against terrorism. Drawing from the ICIJ’s database of U.S. aid assembled from Freedom of Information Act requests and ICIJ reporting in East Africa, here are the basics of what happened in the three countries.

Kenya: In an interview, former U.S. Ambassador William Bellamy estimated that of about $100 million allocated by the U.S. for a new anti-terrorism initiative in East Africa, Kenya would receive $30 million to $40 million. ICIJ’s database show that post-9/11 money from the Foreign Military Financing program to Kenya rose dramatically, to more than $22 million in the three years following September 11 from just $1 million in the three years prior. ICIJ also found that Kenya is one of the top recipients of anti-terrorism training under the U.S. Defense Department’s new Regional Defense Counterterrorism Fellowship Program, receiving more than $1.1 million since 2002.

In North Eastern Province, which abuts the disintegrated state of Somalia, the U.S. military has provided civilian development projects to help the residents, largely Somali Muslims who are pastoral nomads; it has dug wells, built schools and provided medical care. According to press reports, Kenyan authorities also assisted American intelligence and military forces to target terrorist suspects fleeing Somalia after neighboring Ethiopia drove the fundamentalist Supreme Council of Islamic Courts from Mogadishu in December 2006. Kenyan human rights groups also contend that, at the request of the U.S., Kenya assisted in transferring to prisons in Somalia and Ethiopia at least 80 people caught fleeing the fighting in Somalia. The Kenyan government has denied those reports.

Despite U.S. encouragement, the Kenyan Parliament has yet to pass an anti-terrorism law. Opponents said drafts have contained unconstitutional elements and, in the words of a local human rights organization, it “offends national pride and sovereignty to have your laws dictated by another state, however mighty.”

Tanzania: In 2002, the government enacted an anti-terrorism law similar to the one that is stalled in Kenya. And opponents mounted similar critiques, saying it undermined civil liberties, due process and the national constitution. After a spike in military assistance following the 1998 attacks, U.S. military assistance to Tanzania has dwindled, according to ICIJ’s database of military aid and assistance.

Uganda: Uganda has received only a modest boost in U.S. military aid, according to ICIJ’s database. Prior to 9/11, it received no Foreign Military Financing dollars; in the three years after 9/11 it received almost $2 million. Nonetheless Uganda was quick to not only enact an anti-terrorism law but also to apply it to arrest political opponents, crack down on independent journalists and suspend due process.

In Uganda, law denies rights

Uganda’s 2002 Anti-Terrorism Act criminalizes aiding and abetting terrorism, establishing terrorist organizations and supporting, financing or carrying out acts of terrorism. It also grants the government wide powers to eavesdrop on terrorist suspects.

“The Ugandan media has been awash with reports about suspects who are arrested under the Anti-Terrorism Act and blatantly denied their fundamental human rights as enshrined in the country’s constitution,” Moses Sserwanga, a journalist and lawyer working with the Monitor newspaper in the capital of Kampala, told ICIJ. Suspects are often detained in unmarked locations without access to legal counsel, according to a report by the local human rights group Foundation for Human Rights Initiative — since denied by the Ugandan government.

Some of the first groups to be declared terrorist organizations under the new law were long-standing violent anti-government groups such as the Lord’s Resistance Army (LRA), which most outside experts consider a traditional insurgency group rather than a foreign terrorist organization.

In a paper presented to an International Commission of Jurists conference in Nairobi in 2007 on how the war on terror has affected human rights, Simon Peter Mutegeki of the Foundation for Human Rights Initiative said the situation in northern Uganda — the LRA stronghold — “has created room for human rights violations by government forces under the guise of fighting terrorism. Soldiers in the national army have raped, beaten and arbitrarily detained and killed civilians in camps with brazen impunity.” Mutegeki also says the government has failed to prosecute military officers who commit such atrocities, instead transferring them to other areas where the abuses continue.

Uganda’s chief justice, Benjamin Odoki, has condemned misusing the justice system to fight political battles. Terrorism suspects are increasingly tried before both civilian and military courts, subjecting them to double jeopardy, which the Ugandan constitution prohibits.

The government has also employed the anti-terrorism law to detain journalists and destroy or confiscate their equipment, particularly in areas where the LRA is active. In defending those tactics, Ugandan government officials say that by publishing information journalists are in essence promoting terrorism or encouraging terrorists — which makes them subject to criminal charges under the Anti-Terrorism Act, according to Charles Onyango-Obbo, a Ugandan journalist working in Nairobi for The Nation newspaper.

In Kenya, FBI joined interrogation

In Kenya, lack of anti-terrorism legislation didn’t prevent rounds of arrests in coastal towns and in Nairobi in response to the Kikambala and Mombasa attacks.

Amnesty International conducted a comprehensive investigation of the arrests and detentions and condemned them for violating international human rights standards. The group reported that dozens of suspects were detained for long periods at undisclosed locations and denied legal counsel, and that in some cases police also detained and harassed suspects’ family members. Many reported being interviewed by foreign interrogators, feeding speculation that they were American agents or Israeli agents investigating the attack on the Israeli airliner. Mao Tsetung Maobe, a lawyer who represented some of the Kikambala suspects in court, told ICIJ he witnessed foreign agents harassing and intimidating detained suspects.

One Kikambala bombing suspect, Mohammed Ahmed Surur, was arrested on May 31, 2003, and reported later that he was blindfolded and driven to Nairobi, where he was interrogated by 10 police officers. According to Surur’s sworn affidavit, obtained by ICIJ, eight of the officers were white, leading him to believe they were either U.S. or Israeli agents. An American diplomat in Nairobi confirmed to ICIJ that the FBI took part in the interrogation with the consent of Kenyan authorities.

“One white officer seated on my left grabbed me by my neck and banged my head on the table,” Surur said in the affidavit, adding that he was forced to sit in an electrically charged chair in an effort to coerce him to sign an incriminating statement. When he initially refused to sign, “one white officer switched on the computer, and I felt a lot of current running into me causing me excruciating pain.” When the interrogators failed to connect him to the Kikambala bombing, Surur was abandoned in the streets of Nairobi without any formal charges.

Seif’s ordeal

Which brings us back to the case of Kubwa Mohammed Seif, who was charged with murder in the Paradise Hotel bombing just weeks after Ambassador Carson complained of inaction by Kenyan authorities.

Seif, an elected member of the Lamu municipal council, told ICIJ in an interview that his ordeal began on February 26, 2003, when he was stopped by four police officers who were looking for his father. Seif says he took them to the village of Siyu on Pate Island, where his father lived. The officers immediately arrested the father, Kubwa Mohammed, and took him to the Lamu police station.

The next day, Seif and his sister, Swalla Kubwa, were arrested as well; Seif said no one told any of them why they had been detained. The following day, all three were taken to the Mombasa police headquarters and shown photographs of various people that they were asked to identify. Seif said all three knew one man, Abdul Karim, who had been a local soccer player and madrassa (Muslim religious school) teacher in Siyu — and who had married Seif’s stepsister a month after the Paradise Hotel bombing.

A day later, a family attorney, Kheleef Khalifa, went to the police station, but he told ICIJ he was denied access to his clients. Later that evening, the police flew the three to Nairobi. “In the cell, I was alone,” Seif told ICIJ. “I had no warm jacket and there was no blanket or mattress. Nobody knew where I was. I was very frightened. I cried and prayed.”

After being detained for 10 days in Nairobi, the three family members were released without charges. But weeks later, Seif and his father were arrested again and taken back to Nairobi, where Seif said individuals who appeared to be foreign agents interrogated them. After two weeks of interrogation, he says, they were charged with “harboring a terrorist suspect.” Several others were also charged, including Said Sagaar Ahmed, another madrassa teacher, and Aboud Rogo Mohammed, a Muslim cleric in Mombasa. Eventually they were released on bail.

Then Ambassador Carson spoke out, complaining that Kenya was doing little to arrest and prosecute terrorism suspects, that “not a single conviction” had been achieved. The next day Seif was arrested for the third time.

“I went home at around 10:30 p.m. and found my house surrounded by many police officers,” he told ICIJ. “They had searched every nook and cranny of my house. My children were all wailing as I was arrested and hurled into a police car.” Kiraitu Murungi, then Kenya’s minister for constitutional affairs, announced in the Daily Nation newspaper that Paradise Hotel bombing suspects would shortly be charged and brought to court.

Seif and his father and two other suspects were charged with murder the following day. Their attorneys argued that the charges were baseless and were brought only because of American pressure. The prosecution is intended “to satisfy specific demands by a specific country,” one of their attorneys, Mao Tsetung Maobe, told the court. Subsequent mass arrests up and down the Kenyan coast, as well as in Nairobi, led to public demonstrations by local Muslim groups.

The trials of Seif and his father and the others were protracted, lasting months. As they progressed, the prosecution withdrew the murder charges, reducing them to “conspiracy with intent to murder.” At one point the defendants were also charged in a conspiracy to shoot down the Israeli aircraft at the Mombassa airport as well as in a plot to bomb the American Embassy in Nairobi.

In the end, all suspects were acquitted for lack of evidence. No one has yet been charged in the hotel bombing or the missile attack on the Israeli aircraft. In late March 2007, the Pentagon announced that a terrorist suspect apprehended in East Africa, Abdul Malik, had admitted to a role in planning the Mombassa attacks and had been transferred to the U.S. naval detention facility at Guantánamo Bay, Cuba.