Liboi is a Kenya border crossing near the southern tip of Somalia, where Ethiopian and Somali government troops have been hunting for Islamic courts fighters.
Kenyan officials have said that Ahmed has been flown to Nairobi, the Kenyan capital, and is being held in a hotel.National reconciliation
"He is the public face of the Islamic courts and is increasing being seen as crucial to any national reconciliation effort in Somalia ... this is why, diplomatic sources say, he is being held in a hotel and this is why he is under US protection," Mohammed Adow, Al Jazeera's correspondent in Mogadishu, said.
An official with the US embassy in Nairobi denied reports that Washington had any involvement in Ahmed's presence in Kenya.
"Peace is possible if the interests of US and the Ethiopians are removed"
Ahmed, Bossaso, Somalia
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"The United States is not holding or interrogating or protecting Sheikh Sharif," the official told the AFP news agency. "We were not involved in his capture or surrender."
The United States sees Ahmed as a moderate in the Islamic Courts movement which formerly vowed to topple the Somali government and to extend its system of Islamic laws across all Somalia.
Michael Ranneberger, the US ambassador to Kenya, whose brief includes Somalia, met him in Nairobi last year after the Islamic Courts seized Mogadishu to urge them to practise moderation.
Ahmed shared the leadership of the Union of the Islamic Courts with Sheikh Hassan Dahir Aweys, who was chairman of the court's legislative council.
Ethiopian troops came under fire again on Monday as they carried out searches in the south of the capital, residents told the AFP news agency that at least four civilians were killed in the ensuing gunbattle.
The searches were being conducted after an ambush on an Ethiopian convoy at the weekend which also resulted in a deadly gunbattle.