The assassination of outspoken Islamic cleric Sheikh Aboud Rogo in Mombasa two weeks ago set off days of violent protests in the Kenyan port city, with several deaths and attacks on churches.

The riots brought into focus the deteriorating state of Christian-Muslim relations in Kenya and the rising rage of the country’s unemployed youth, but the killing also capped a sinister trend of murders and disappearances of Muslim leaders across East Africa.

READ: Violent protests erupt over Muslim cleric’s killing

Altogether, the disappearances and killings of Muslim leaders in East Africa fit a pattern that would have set the alarm bells ringing by now if it had involved Christian leaders.

A precise figure is hard to obtain or independently verify and corroborate, but some Muslim sources and rights groups monitoring the body count, claim nearly a dozen may have been killed in the past one year alone, often in circumstances uncannily similar to the killing of Sheikh Rogo.

Mr Rogo was killed by unknown assailants in a morning drive-by shooting in Bamburi, Mombasa, while in a car with family members.

Although his family claims that his death was an assassination by the police, Kenyan security agencies have denied involvement in the killing.

READ: (Opinion) Who killed Rogo? Not I, said the policeman

A team headed by the Director of Public Prosecution Keriako Tobiko has since been set to investigate the killing.

In Uganda, there has been a recent wave of similar killings, although arrests by police points towards criminal rather than political motives for the murders.

What is happening today is the culmination of a silent but deep crisis that has enveloped the Muslim community in East Africa since the 1998 terrorist bomb attacks on the US embassies in Nairobi and Dar es Salaam.

That crisis has been intensified by the war in Somalia, involving on the one hand the Somali transitional government and the East African forces from Uganda, Burundi, and Kenya, who form the bulk of the African Union peacekeeping force Amisom, and the Al-Qaeda affiliated Al Shabaab militants on the other.

Al Qaeda was blamed for August 1998 bombing of the US embassies, in which 219 people were killed and 5,000 injured in Nairobi, and 11 killed and over 70 injured in Dar es Salaam.

This creeping crisis should concern regional leaders, given the surging Muslim numbers in the EAC region.

While most countries in the region tried not to tar all Muslims with the terrorist brush, some politicians and hard-line evangelist Churches sought to portray Muslims and Islam as a danger.

Kenya participated in the rendition of suspected terrorists, all of them Muslims, to Guantanamo, the controversial US detention centre, as well as to Ethiopia, Eritrea, Somalia and other countries.

“I was not told of any crime, there were no charges. I was just picked up and told I was a terrorist,” said Al-Amin Kimathi, a Kenyan human-rights activist who was arrested in Uganda and released after one year in custody at the Luzira Maximum prison.

In Guantanamo Bay, Kenyan Mohammed Abdulmalik is rotting in detention five years after he was taken to the detention facility, after the US accused the father of three of involvement in a 2002 attack on an Israeli-owned Kenyan beach hotel, in which 13 people died, and an unsuccessful attempt to bring down an Israel-bound plane in the coastal city of Mombasa.

Anti-terrorism laws

In the wake of the 1998 embassy bombings, the EAC countries moved to pass anti-terrorism laws, with Tanzania being the first to push through the stringent Prevention of Terrorism Act, No 21 of 2002.

In the same year, Uganda passed its Anti-Terrorism Act. Ironically Kenya, the country most affected by the 1998 blasts, has never passed an anti-terror law.

An anti-terrorism Bill that was first floated in 2003 was withdrawn in the face of widespread criticism; it has recently been revived as the Terrorism Prevention Bill 2012 and is before the Cabinet.

“We found some sections of the law like the clause that gives powers to the police to detain people without consulting with the courts or any other third party, making them  both the judge and executioner, to be punitive and infringing on basic human rights,” said Fazul Mohammed, secretary of the Association of Muslim Organisations in Kenya, who has presented the views of Muslims to the Kenyan Cabinet for consideration.

Nevertheless, even in the absence of a specific law, Muslims say their human rights are being systematically infringed.

“Whatever is currently happening in Kenya is far worse than whatever is taking place in Uganda and Tanzania, countries that have anti-terror laws,” said Hussein Khalid, executive director of Muslims for Human Rights (Muhuri), adding that the greater Horn of Africa is now the “worst place to be a Muslim in Africa.”

While terrorism has led to a rising anti-Islamic rhetoric among Christian communities and governments, or on the opposite side, a rush to avoid Christian-Muslim conflict, the response by Muslims has been more varied and complex.

One has been the rise of radical clerics who argue that Islam is under siege by an international conspiracy, led by the US.

“The Americans are attacking us because we are Muslims and we believe in the Koran. Would they do this to us if we were Christians?” asked Said Abubaker Shariff Ahmed alias Makaburi, a close friend of the late Sheikh Rogo.

In the middle has been the growth of moderate Islamic groups who make the point that violence is un-Islamic and is condemned by the Koran, contrary to the propaganda that Islam espouses violence.

On the right, are the traditionalists, who want to keep Islam out of politics, either radical or moderate, and to preserve the privileges of the mosques, for example land that they got from old Independence settlements.

These waters have been churned further by Middle East governments like Saudi Arabia pumping money into the region to support various Islamic causes and groups, and East African governments trying to hijack the leadership of Muslim umbrella groups like the Uganda Supreme Council.

In Uganda’s case, Middle Eastern money and government meddling have sparked off internal rivalry that is thought to be behind the unsolved murders of three Muslim leaders in the past one year alone.

In 2010, following the July World Cup final bombings at two club events in Kampala in which over 70 people were killed, Ugandan police arrested over 20 terror suspects, most of them Muslims, provoking uproar within the community. The attacks were claimed by Al Shabaab, which said it wanted to punish Uganda for its role in Amisom.

Then, as today, the Uganda army formed the largest element of the Amisom force. Burundi, which was still the only other country along Uganda that had troops in Somalia, had its own scare. Rwanda intelligence intercepted suspected Al Shabaab bombers at the Burundi-Rwanda border as they headed to Bujumbura.

This year, a cleric by the name Sheikh Karim Sentamu was shot dead in the evening of April 23 in Kampala shortly after he had led evening prayers in a city mosque.

Investigations by police have neither yielded clues or suspects. In June, another Muslim leader, Sheikh Abubaker Kiweewa, was shot dead as he prepared to close his retail outlet for the day in Kyanja, a city suburb.

An imam in Bugiri, Sheikh Yunusu Abubakari, was shot dead earlier this month on the eve of Idd celebrations.

Suspects confessing to involvement in the killings of Sheikhs Abubaker and Yunusu have since been arrested and linked to a notorious robbery gang in Kampala.

But these robbery-related explanations of the killings have not mollified Muslims and claims abound of government involvement in some of the killings.

In a meeting with Muslim leaders, President Yoweri Museveni said he believed Sheikh Sentamu had links with Jamir Mukulu, an ADF rebel leader, hinting this could explain his death, but this view has been challenged by a local MP.

“It is an attack on Muslims; the shooting of Sentamu, Kiweewa and the sheikh from Bugiri was premeditated,” said Ibrahim Semujju Nganda, the Kyadondo East MP.

In Tanzania, the leader of the Islamic Revival Forum, (Uamsho), Shaykh Farid Hadi Ahmad, was arrested and charged on July 22 in Zanzibar.

Uamsho, or “Islamic Awakening,” is among the most vocal of Zanzibar’s small radical organisations. Registered as an NGO in 1999, Uamsho is active almost exclusively in Unguja Island’s Stonetown, and consists of a few dozen relatively young clerics with a Saudi Wahabbist orientation.

While the Muslims in Kenya, Tanzania, and Uganda seem to be in turmoil, the scene is quieter in Burundi and Rwanda. In Rwanda, unlike the Catholic Church, the Muslim community has been able to rise above the Hutu-Tutsi divide.

In the 1994 genocide Muslim families and leaders hid and sheltered many Tutsis and opposition Hutu who were being hunted by the Interahamwe killer militia.

Without a single voice, and if Muslims remain divided over control of Middle East money, the killings and abductions are likely to continue.

How it all ends, no one knows, but a backlash from younger, more militant youth, could give regional governments a future headache they can avoid now by speedy and more transparent resolutions to the killings and abductions.

The alternative is grim: In East Africa, different faiths have co-existed peacefully for centuries; the region has never seen large-scale religious riots of the sort that routinely kill thousands in Nigeria or India. It is the kind of precedent that East Africa emphatically wants to avoid.