President Abdullahi Yusuf Ahmed was unhurt after assailants blew up a car outside parliament and fought with security forces.
The attack occurred around midday in Baidoa, the temporary seat of the transitional administration, amid heightened tension between the weak government and Somalia's powerful Islamist movement.
But at least 11 people - five members of President Yusuf's entourage, including his younger brother, Abdulsalam, and six presumed attackers - were killed, and at least 18, including nine presidential guards, were wounded, officials said.
The Somali government later appealed for international help to probe the suicide bombings, as authorities continued to interrogate two suspects arrested after the alleged suicide bombers fought security forces.
'Terrorists' blamed for attack
Prime Minister Ali Mohamed Gedi blamed the attack on "terrorists" organised within the lawless country, which has been wracked by anarchy and without a functioning central administration for the past 16 years.
"The attack was carried out by terrorists who wanted to kill the president, his bodyguards and locals," Mr Gedi told reporters in Baidoa, about 250 kilometres northwest of Mogadishu.
"These terrorists were sent to Baidoa and were organised somewhere in Somalia to derail security in this town," he said, adding that two of the attackers had been arrested and an unknown number of others were being pursued.
Somali Foreign Minister Ismail Mohamed Hurre said the perpetrators of the "well-planned attack to kill the president" were linked with the weekend murder of an elderly Italian nun in Islamist-held Mogadishu.
He was referring to the killing on Sunday of Sister Leonella Sgorbati, 65, who was gunned down by two men at a charity hospital in the capital amid fury over Pope Benedict XVI's recent comments about Islam.
Islamist officials condemned the attempt on President Yusuf's life as well as the slaying of the nun, for which one suspect is in custody.
"We very much condemn the deaths of the people in Baidoa," Abdurahim Ali Muddey, a spokesman for the Supreme Islamic Council of Somalia (SICS), told news agency AFP in Mogadishu. "Those who carried out this attack are the enemies of Somalia."
The United Nations and European Union also condemned the attacks, particularly the one on President Yusuf, which they said appeared aimed at derailing efforts to ease tensions between the government and the Islamists.
"We condemn this attack on the peace process and call on all Somalis to resolve their differences peacefully," they said in a statement issued in Nairobi.
Witnesses said the attack began when a remote-controlled car bomb detonated outside the parliament building as the president's convoy was leaving after a speech, killing five people and sending a huge fireball into the sky.
Six purported assassins were then shot dead in a gun battle with security forces, according to witnesses who reported hearing at least one other powerful blast.
Lawmakers said no one inside the parliament building, a converted warehouse, had been injured and that after the attack, the legislators had approved Mr Yusuf's nominations for a new cabinet to be headed by Mr Gedi.
Sides deeply divided
The new slate is hoped to ease fractious government infighting that has left the administration unable to exert control over much of the country and seriously challenged by the rise of Somalia's Islamist movement.
The Islamists, some of whom have been accused of links to Osama bin Laden's al-Qaeda network, seized Mogadishu from warlords in June after months of fierce fighting and have since rapidly expanded their territory.
They are now in control of much of southern Somalia where they have begun enforcing strict Sharia law in what many see as a direct threat to the government and fuelling fears of a Taliban-style takeover.
Despite an interim peace accord reached earlier this month, the two sides are deeply divided over several key issues, notably the proposed deployment of a nearly 8,000-strong regional peacekeeping force.
The Islamists have vowed to fight any foreign troops if they are sent while the government has repeatedly appealed for the deployment.
Somalia, a Horn of Africa nation of some 10 million, has been without a central authority since it was plunged into anarchy with the 1991 ouster of strongman Mohamed Siad Barre.
Mr Yusuf's government is the latest in more than a dozen attempts to restore stability but since it was created two years ago, it has been wracked by infighting and there have been two unsuccessful attempts to kill Mr Gedi.