Abdullahi Yusuf sacked his popular prime minister on Sunday
Nearly 120 Somali MPs have voted to start impeachment proceedings against President Abdullahi Yusuf, accusing him of being a "stumbling block to peace".
He must now appear before parliament to defend himself. The motion would need a two-thirds majority to succeed.
The move in Baidoa comes a day after the president named a new prime minister in defiance of parliament.
MPs also supported a UN-backed peace deal between the transitional government and Islamist rivals.
But the Islamist al-Shabab insurgent group that controls much of southern Somalia has not signed up to the agreement.
President Yusuf told AP news agency from the seat of parliament in Baidoa: "It cannot be true that I'm an obstacle to peace. It is propaganda."
The resolution to impeach him - which alleged he had violated 14 articles of the Western-backed transitional government's constitution - had the support of 117 legislators in the 275-member parliament.
President Yusuf is accused of illegally printing money, nepotism, behaving like a dictator and failing to push the peace process forward after four years as president.
He is also charged with side-lining some of the communities.
Correspondents say this is coded language referring to the increasingly bitter clan rivalries that have deepened under his leadership.
The president's sacking of the prime minister sparked protests
President Yusuf's biggest miscalculation appears to have been a decision to sack Prime Minister Nur Hassan Hussein and his cabinet on Sunday, they say.
Lawmakers soundly rejected President Yusuf's unilateral decision - saying it needed parliament's approval - and voted to keep Mr Nur as prime minister.
President Yusuf and Mr Nur had clashed in recent months over attempts to deal with the Islamist-led armed opposition.
Mr Nur was chairman of Somalia's Red Crescent Society during many years of conflict before being named prime minister.
On Tuesday, Kenya announced it would impose sanctions on Mr Yusuf and his family because it also said he was an obstacle to peace.
The BBC's Mohamed Olad Hassan in the capital, Mogadishu, says it is not clear if the impeachment move will work as Somali lawmakers can be very unreliable in their voting.
'Only option left'
Mustafa Duhulow, an agriculture minister who topped the list of MPs behind the impeachment motion, said a number of lawmakers were in Mogadishu, or even out of the country.
"He's the president. He should be the one who's working very hard to bring the unity to Somalia, reconciliation to Somalia. Now he doesn't want to do that," he told the BBC World Service's Focus on Africa programme.
"The president is the problem of the country. We've tried everything… the only option left for us is to impeach him."
Some analysts fear a power vacuum after the Ethiopians leave
Correspondents say Somalia's government badly needs a unified front if it is to find peace with hardline Islamist insurgents who now control almost all of southern Somalia.
In parliament on Wednesday, MPs also endorsed with a show of hands a reconciliation deal between the more moderate Islamist Alliance for the Re-liberation of Somalia (ARS) and the transitional government, sponsored by the UN in neighbouring Djibouti.
That agreement requires Ethiopian forces - which helped government forces drive Islamist forces from Mogadishu two years ago - to pull out in just over two weeks.
A small African Union peacekeeping force has indicated it may leave with the Ethiopians unless it gets reinforcements.
About one million people have fled their homes - many after fierce fighting in Mogadishu between Islamists and the Ethiopia-backed government forces.
Somalia has not had a functioning national government since 1991 when warlords overthrew the regime of President Mohamed Siad Barre and then turned on each other.