(Updates with U.S. State Department declining comment)

By Jeremy Clarke

NAIROBI, March 31 (Reuters) - A U.S.-based human rights group has accused the United States, Kenya and Ethiopia of running a secret detention programme targeting people fleeing a war on hardline Islamists in Somalia.

Human Rights Watch (HRW) said it had documented the "arbitrary detention, expulsion and apparent enforced disappearance of dozens of individuals who fled the fighting" in Somalia earlier this year.

"Each of these governments has played a shameful role in mistreating people fleeing a war zone," HRW's deputy Africa director, Georgette Gagnon, said in a statement obtained by Reuters on Saturday.

"Kenya has secretly expelled people, the Ethiopians have caused dozens to 'disappear', and U.S. security agents have routinely interrogated people held incommunicado."

Officials of the three governments in the region were not immediately available for comment. In Washington, the U.S. State Department declined to comment.

This week, Somali government troops backed by Ethiopian forces stepped up attacks against what they call the armed remnants of a hardline Islamist movement ousted from Mogadishu in fighting over the New Year. Ethiopia and the United States have accused the Islamists of having links to al Qaeda.

The arrest of scores of Somalis trying to enter Kenya in early January after the Islamists fled Somalia's capital has angered local rights groups and Kenyan Muslims.

HRW said several were interrogated by U.S. agents before at least 85 were secretly deported back to Somalia in what the group said appeared to be a "joint rendition operation" of individuals of interest to Nairobi, Addis Ababa and Washington.

HRW said it recognised Kenya might have valid security concerns about foreigners seeking refuge, but these must be handled in line with international law and human rights.

It said many of those deported to Somalia were later transferred to Ethiopia, where they "effectively disappeared".

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