03/25/2014 11:47 am ET Updated May 25, 2014

Trouble Looms as Kenya Struggles to Combat Terrorism

Kenya's fear of terrorism, and its poor response, is plaguing the large port city and tourism hub of Mombasa.

In a Mombasa courtroom earlier this month, amidst protests from the prosecution that cameras and notepads be barred for security reasons, the presiding judge issued a summons for the Mombasa County Police Commander to answer questions about the disappearance of a 42-year old man, Hemed Salim Hemed. Helem was last seen (and photographed) being carted away by police on February 2, when Kenyan authorities raided the prominent and controversial Masjid Musa Mosque.

Authorities said they conducted the raid because people had gathered at the mosque to discuss jihad. Some who were there do not dispute this, though they maintain they did nothing unlawful. Others say they came to enjoy a free lunch, which could account for the high number of children who found themselves spending nights in prison.

Altogether, the police made over one hundred and twenty arrests. Police beat children and at least one police man was killed in ensuing violence. There are allegations that the police shot dead up to eight people, though the police say the number stands at two. The majority of those detained are now free, released without charge. Meanwhile, Hemed is nowhere to be found, with police giving inconsistent accounts that he escaped.

The raid went largely unreported by international media outlets, despite Kenya being a key U.S. and U.K. partner in the fight against Al-Shabaab. The raid is also one in a series of incidents that reveal the troubled times that terrorism, and Kenya's response to terrorism, is causing for Mombasa and Kenya generally.

While the media's gaze may sharpen on Somalia, the port city of Mombasa, defined by its majestic beaches and relaxed atmosphere, is becoming increasingly known for acts of terrorism, counterterrorism human rights abuses, and -- most recently -- growing tensions between violent Muslim youth and the old-guard. Any one of these problems is destructive on its own, but with all three existing, Mombasa -- Kenya's second biggest city and a tourism hub with a majority Muslim population -- is going through particularly turbulent times.

State House may be applauding its efforts in Somalia and occupied with the International Criminal Court, but in the wake of the government's embarrassing response to the September 2013 al-Shabaab-claimed attack on the affluent Westgate shopping mall in Nairobi that killed 67, Kenya's leadership must also feel at a loss for its inability to get a handle on the situation in Mombasa. That security forces conducted a mid-day raid on a mosque demonstrated the government's willingness to push the envelope on what the people in the Coast would accept as legitimate counterterrorism measures.

While this public demonstration of force was new, human rights activists say it was not unpredictable given the beatings, disappearances, and alleged unlawful shootings of suspected terrorists that came before. A high-ranking Kenyan counterterrorism official based in Nairobi told me last year, "In this work you can't go by the book." "What do you do if no one gives you evidence?" he asked, then answering himself, "This is why there is Guantanamo Bay."

The BBC reported an even more candid admission of an Anti-Terrorism Police Unit officer, who disclosed, "The justice system in Kenya is not favourable to the work of the police...So we opt to eliminate them. We identify you, we gun you down in front of your family, and we begin with the leaders."

In August 2012 and October 2013, the government may have pushed too far, with Mombasa filling with smoke, teargas, and bullets, as people took to the streets to accuse the government of either having a hand in, or at least failing to prevent, the murder of two prominent and controversial clerics, Aboud Rogo (2012) and Ibrahim Ismael (2013, also known as Ibrahim Omar Rogo). The violence, which was also aimed at churches, took on a religious character that gave it a potential to spiral out of control. Fortunately, the situation quickly cooled -- largely due to outspoken calls for calm by Muslim and Christian community leaders -- and Mombasa re-emerged as the reputable laid-back port city it is known for being.

The respite was brief however. Last Sunday, March 23, men opened fired on church-goers in Lakoni, just outside Mombasa city, killing at least six people. Also this month, Kenyan police reported that they arrested three terrorists in Mombasa and recovered car bomb, grenades, a gun and munitions. Headlines ran, "Shocking cache of terror arsenal found in Mombasa," and the media reported that FBI bomb experts were at the scene. Kenya security force killings, beatings, and disappearances, of which Hemed Salim appears to be the latest, also continue. There are regular concerns that people may again take to the street.

Adding to these problems, there is now a new palpable sense of tension in the Mombasa air between the more "radicalized" youth and the more tempered clerics. The latest incident was on March 13, when violent youth with knives and stones assaulted a Muslim cleric, Ali Bahero, for, presumably, ideological differences. Ali, his Islamic attire smeared with blood, leaned slumped with his back against a wall before being taken to an intensive care unit.

This attack followed other altercations that teetered on the edge of serious violence. In November 2013, the Kenyan daily The Star reported that hundreds of Muslim youths armed with knives stormed Sakina mosque in the Majengo neighborhood of Mombasa and "ejected imams from the pulpit." Human rights activists, traditionally concerned about the government's response to their criticisms, are now also fearful that they are drawing the gaze of the youth for advocating peaceful and moderate solutions.

In the past, religious leaders and interfaith dialogue calmed violent emotions before they turned from street violence to more protracted violence. Today, the old-guard may be losing its ability to dissuade those who use violence to accomplish their goals and respond to the government's inhibitions to commit human rights abuses in its counterterrorism operations. If this is the case, it seems Kenyan security forces will feel increasingly nervous and uncertain about the security situation, which means Mombasa's turbulent times may only worsen.

If this is not enough to handle, some in Kenya's vibrant civil society see the events unfolding in Mombasa as part of a larger government power-grab. Mombasa can be a very inward looking place; and the rest of Kenya often shuns Mombasa as a pestering stepchild. But Kenya's willingness to use excessive force to combat terrorism in Mombasa -- as well as places such as Garissa and Eastleigh -- may be part of a larger pattern to extend government powers while keeping government less accountable to its people.

In 2012, Kenya passed the Prevention of Terrorism Act that granted the state intrusive investigation and far-reaching detention powers that many in the Muslim community fear will be misused and abused. There have been legislative proposals to dilute police accountability and to allow the police to use lethal force in circumstances beyond what international law permits. New legislation placed tight regulations on the media and proposals were made to place severe restrictions on civil society organizations.

It is now the hottest of seasons in Mombasa. Fortunately, on March 15, heavy showers from the night before helped to cool a large room in the Royal Castle Hotel packed with people who came to hear human rights activists describe why Kenya's counterterrorism tactics and the accompanying human rights abuses are counterproductive. The event was hosted by the Mombasa-based organization Muslims for Human Rights, which I have worked close with and the Open Society Foundations, amongst others, supports.

A woman, Rehema, spoke of her husband's disappearance by Kenya's authorities in December 2012. Others described how the police's February raid on the Masjid Musa Mosque had infuriated the community. Human rights defender Al-Amin Kimathi contrasted the events to Chief Justice Willy Matunga's story about how during the Mau Mau civil war in the 1950s, British soldiers resisted entering a church in which fighters took refuge. Hussein Khalid, the executive director of Haki Africa, was similarly critical. But he also noted that a few years ago he never would have predicted that a Mombasa judge would badger security officers over the disappearance of a terrorist suspect such as Hemed Salim Hemed.

The event went off without incident, but it was a microcosm of what Mombasa is going through. Knowing the likelihood that security agents may be in the crowd, the event was hosted in a well-known location where both the attendees and authorities may have felt compelled to keep their tempers low. Bishop Alfred Obuya sat on the panel (as did I) to demonstrate the interfaith concerns that human rights abuses raise. And those who advocate non-violent means to solve Mombasa's problems delicately delivered a message of how it is important that however severe the dissatisfaction is with their government, that it does not divide the community, knowing that some in the crowd may favor violence over legal recourse and dialogue.