Al Qaeda militants are operating with "great comfort" in Somalia, providing training and assistance to a radical military element loyal to the Islamic group that controls most of southern Somalia, a senior State Department official said Wednesday.

Jendayi Frazer, who heads the department's Africa bureau, said a priority U.S. goal is the capture of three militants wanted for the bombings of U.S. embassies in Kenya and Tanzania in 1998 and a hotel in Kenya in 2002. The three are from Sudan, Kenya and the Comoros Islands, located off Africa's east coast.

"We're continuing to work with all sides in Somalia to try get those terrorists turned over and to prevent Somalia from becoming a safe haven," Frazer told a small group of reporters.

Complete coverage is available in FOXNews.com's Africa Center.

She emphasized that the Al Qaeda presence goes well beyond the three suspects.

The administration has looked on with anxiety as Islamic militants, operating under the umbrella of the Union of Islamic Courts (UIC), have expanded their zone of influence in the country while marginalizing a secular government that lacks authority despite the backing of the United Nations and the United States.

The secular authority, known as the transitional federal government, is based in the western Somali town of Baidoa, unable to expand its reach further.

The administration supports the creation of an African force, totaling a battalion or two, to train and protect the transition government. The goal is to establish a balance in Somalia that would convince the Islamists that a military victory is impossible, thus creating conditions for a negotiated settlement between the two.

The African Union and the Intergovernmental Authority on Development, a seven-nation East African group, originally proposed deployment of an African force in Somalia.

The Islamists said in June they had no interest in forming a government but their actions since then suggest otherwise, the administration believes. The rise of the UIC over the past six months has alarmed non-Muslim countries throughout East Africa and generated fears of armed conflict throughout the region.

From the outset, the United States has supported a dialogue between the Islamists and the transition government.

In a statement Tuesday night, the State Department said the "continued military expansion by the UIC has prevented this dialogue from moving forward and has created the need for deployment of a regional force.

"The force will deter further aggression against the transition government, create the required space for dialogue and stabilize the situation."

The only country that has volunteered troops for the African force thus far is Uganda.

Get complete coverage in FOXNews.com's Africa Center.