It is alleged they were questioned by US and British officials.
Flight manifests seen by The Independent show that three charter planes left Nairobi for Somalia's capital Mogadishu, and Baidoa, the seat of parliament, in January and February, carrying around 80 people suspected of links with al-Qa'ida. The flights left at night, and the manifests appear to have been filled in hastily with many of the details, including the plane's destination, left blank.
Several of the suspects are understood to be held in underground prisons at Mogadishu airport where they are held shackled to the wall. Most have since been sent on to two detention facilities in Addis Ababa. Ethiopia has been accused of routinely torturing political prisoners. A further 50 or 60 people accused of belonging to Ethiopian rebel groups fighting alongside Somalia's Union of Islamic Courts were sent directly to Ethiopia.
Fighting has reignited in Mogadishu this week following Ethiopia's lightning offensive at the end of last year, which drove the Somali Islamists from the capital. On Wednesday at least 21 people were killed and more than 120 wounded in clashes that led to the burning of five uniformed soldiers, who were either Somali or Ethiopian.
The televised incident was reminiscent of events of 1993 when Somalis dragged the corpses of US soldiers through the streets, hastening the US withdrawal from the country.
The suspects deported from Kenya were interrogated beforehand by American FBI officials in Kenyan prisons, where they were accused of having links with al-Qa'ida.
"This is extraordinary rendition," said Maini Kiai, chairman of the Kenya National Human Rights Commission. "Britain and America are involved in interrogating suspects."
Following the US-backed invasion of Somalia by Ethiopian troops, thousands of Somalis have tried to escape the violence by crossing the long, porous border with Kenya. Many of those caught on the Kenya-Somalia border were accused of belonging to the Islamic Courts and refused entry.
At least 150 of those who managed to get through were detained by Kenyan police, including 17 women and 12 children, one a baby of seven months. Many needed medical attention but did not receive it, including a pregnant Tunisian woman who had a bullet lodged in her back.
All were held in Kenyan prisons for several weeks without access to lawyers and family members. As well as being interrogated by the FBI, human rights groups in Nairobi also claimed British officials were involved.
"The Americans had direct access to the prisoners, one on one," said Al-Amin Kimathi of the Muslim Human Rights Forum, adding that US diplomatic vehicles carried the suspects from Nairobi police stations to be questioned.
"Senior Kenyan police officers told us they had nothing to do with the operation," said Mr Kimathi. "It was out of their hands."
Four of the people taken to Somalia were British. But the day after they arrived in Mogadishu, they were questioned by British diplomats then released.
The US has claimed that Somalia's Islamic Courts, which controlled much of the country until December, was run by an al-Qa'ida cell. Ethiopian troops, backed by US intelligence and logistical support, overpowered the Islamic Courts within a few days of fighting at the end of last year. An interim Somali government, which had been confined to its base in Baidoa, has since taken control of Mogadishu, but guerrillas linked to the Islamic Courts have launched an insurgency with almost daily attacks against government and Ethiopian troops. Ugandan peacekeepers, operating under the auspices of the African Union (AU) have also been subjected to attacks since they arrived in the capital last week.
One diplomat who follows events in Somalia closely said reports of interrogation by US officials were "highly plausible". The deportation of the foreign nationals was "one of the prices we pay for the situation we are in".
Anger over the treatment of Kenyan Somalis trying to cross the border has intensified. Groups based in Mombasa have threatened to disrupt this weekend's world cross-country championships. The US embassy in Nairobi has issued a terror alert, warning that an attack may be carried out during the event.
Descent into chaos
October 1993: Two US Black Hawk helicopters shot down over Mogadishu. Rescue leaves 18 US soldiers dead. Images of dead Americansdragged through streets prompts pullout.
August 2000: Abdulkassim Salat Hassan elected President by tribal leaders and senior figures. He appoints Ali Khalif Gelayadh as his Prime Minister. In October they arrive in Mogadishu.
April 2001: Ethiopian-backed warlords announce intention to form government. More fighting ensues.
August 2004: Transitional parliament inaugurated in Kenya. In October, Abdullahi Yusuf appointed President.
November 2005: Assassination attempt on Prime Minister Ali Mohammed Ghedi. Six die but the PM survives.
February 2006: Transitional parliament meets for the first time since being appointed.
March-May 2006: Fiercest fighting in almost a decade between rival militias in Mogadishu leaves dozens dead and hundreds injured.
June-July 2006: Islamic militias seize control of the capital and southern parts of the country.
December 2006: American-backed Ethiopian and government troops engage and defeat Islamic militias, driving them out of Mogadishu.
March 2007: Pitched battles break out between insurgents and government and Ethiopian troops. Clashes in Mogadishu result in more pictures of the bodies of soldiers being dragged through the city.
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