The parliament opened its first session on home soil since relocating from exile last year but warlords who control Mogadishu failed to show because of tensions in the capital.
“This is a historical opportunity for the Somalia parliament, government and the people,” Mr Yusuf told lawmakers gathered in Baidoa, about 250 kilometres northwest of Mogadishu.
“Let us choose between serving our people or being put on the bad list of history as people who promoted confrontation among Somalis and lacked the skills to administer a modern Somalia,” he said.
“Somalis are fed up with hostilities, displacement and endless violence. The people want peace, freedom and to live under the rule of law.”
Tensions are high in Mogadishu after clashes between allied warlords and a militiamen attached to the city’s Islamic courts that claimed at least 33 lives and displaced hundreds last week.
Other lawmakers said the parliamentary session, the first inside Somalia since the assembly relocated from exile in Kenya in June, was a good start.
“This is a good start for the Somali parliamentarians if they come together and want to amicably resolve differences through dialogue,” said Abdirahman Iddi, minister of parliament and government relations.
The ceremony was also attended by the United Nations political officer for Somalia, Francois Fall, who said the international community expected the Somali leaders to pursue peace.
Yemen’s President Ali Abdullah Saleh sent a congratulatory telephone message and called on the MPs to work for the unity of the government.
Mr Saleh was a key mediator in truce talks last month between Mr Yusuf and parliament speaker Sharif Hassan Sheikh Adan,
The session was held in a makeshift venue, a former warehouse recently renovated and fitted with sound and air conditioning systems.
Security officials used metal detectors to conduct body searches on those who attendend.
With the exception of presidential security, the MPs were banned by Aden Mohamed Saransor, the warlord controlling Baidoa, from carrying weapons.
The transitional government, formed in late 2004, is Somalia’s 14th attempt to restore a central authority in the war-shattered nation that has lacked a functioning government since 1991.
Since its appointment, the government has been rocked with deep divisions between a faction led by Yusuf and Gedi and another led by Adan and the warlords who control Mogadishu.
The president and his prime minister set up shop in the northern town of Jowhar, about 90 kilometres north of the capital, because of insecurity in Mogadishu.