Also on Thursday, a gunbattle broke out in Somalia's chaotic capital, killing two people and wounding four, despite a fragile weekend cease-fire meant to end a surge of violence.
The latest fighting between a secular alliance of local commanders and Islamic militias happened in northeast Mogadishu, prompting residents to flee the area.
The transitional prime minister, Ali Mohamed Gedi, gave four rebel leaders who are cabinet ministers one week to leave the battle-scarred city and join him at the temporary seat of the transitional government.
"I sent a letter to cabinet members who are in Mogadishu instructing them to come to Baidoa within seven days," Gedi told a meeting of the lawless nation's parliament.
Gedi had threatened to sack the rebel-ministers by Thursday but said he was holding off on a decision in an effort to keep his government, which was formed in Kenya in 2004, together.
The order applies to the national security minister, Mohamed Qanyare Afrah; commerce minister, Musa Sudi Yalahow; religious affairs minister, Omar Mohamud Mohmed; and militia rehabilitation minister, Issa Ali Botan.
All are Mogadishu rebel chiefs and charter members of the Alliance for the Restoration of Peace and Counter-Terrorism (ARPCT), which is fighting forces loyal to the city's 11 Islamic courts.
The ARPCT was formed in February with US backing to curb the influence of the courts and track down on foreign fighters and extremists, including al-Qaeda members, they are allegedly harbouring.
Since then, gunmen loyal to the alliance and the courts have fought three major battles in which more than 200 people, mainly civilians, have died.
Gedi's fledgling and largely powerless government has blamed the alliance and the United States for the fighting, the bloodiest Mogadishu has seen since the country collapsed into anarchy in 1991.
The United States has declined to comment on support for the alliance, but US officials have told AFP that the alliance has received US money and is one of several groups they are working with.
Somali government officials say US backing of the alliance is exacerbating the violence and hindering attempts to pacify and reunify the nation.