President Abdullahi Yusuf decided to accede to the lawmakers' demands to preserve negotiations intended at rebuilding the African country, his spokesman said on Tuesday.
"The president has shown great respect for the constitution and for democracy. He is being flexible and mature and setting a positive example," his spokesman Yusuf Muhammad Ismail said.
The 275-member parliament, meeting in the safety of neighbouring Kenya, voted on Saturday to reject a new government less than two weeks after it was appointed.
Members of parliament said the vote was a protest against a decision by the president to swear in a cabinet without having his prime minister submit it to parliament for approval, as a transitional constitution requires.
Most of the cabinet, consisting of 34 ministers and 54 assistant ministers or ministers of state, were sworn in on 1 December in Nairobi, in the culmination of two years of peace talks held in Kenya.
It is Somalia's 14th attempt at establishing a national government since 1991, when Muhammad Siad Barri was toppled by tribal leaders.
The president re-appointed his prime minister Muhammad Ali Geedi on Monday evening and would submit the appointment to parliament for approval, Ismail said.
Geedi would then select a cabinet and also submit it to the assembly for scrutiny, he added.
Some tribes have complained of
not receiving their rightful share
Ismail also said the re-appointed cabinet would be made up largely, but not entirely, of the same ministers.
The cabinet was meant to be selected according to a formula agreed at the peace talks that gives equal proportions of jobs to the four major tribes and a smaller portion to a minority tribe.
But since the cabinet's announcement, a number of tribes have said that the president had failed to ensure they were given their rightful share of posts.