Somali Prime Minister Ali Mohamed Ghedi has given overpowered Islamist fighters three days to hand in their weapons.
Ethiopian-backed troops took the capital, Mogadishu, a few days ago
The move comes after Somali government forces and heavily-armed Ethiopian troops drove the Islamist militia from areas they had held for six months.
Early on Monday, the militia abandoned their final stronghold, the southern port of Kismayo.
Somalia's government has appealed to Kenya to seal the border to prevent fleeing Islamist forces from crossing.
Kenya had "put the necessary security measures in place along the common border" and its forces were on alert, a statement on the Kenyan government spokesman's website said.
'Misled by terrorists'
Mr Ghedi has set a deadline of Thursday for residents of the capital, Mogadishu, to hand in their weapons or be forcibly disarmed.
"Those who have been misled by international terrorists themselves, those who flew away from the capital city purposely or following the misleading of the terrorists are called upon to come back," he said on Monday.
"The government is providing amnesty for them."
He appealed for humanitarian aid for the country and urged the African Union (AU) to send peacekeepers.
"We would like the military observers and peacekeepers to come in to help us as soon as possible," he told reporters.
Kenyan President Mwai Kibaki has called for a summit of East African countries to discuss the situation, while Ugandan Foreign Minister Sam Kutesa told the BBC that his country was ready to commit 1,000 troops as part of an African regional peace-keeping force.
'Won't stop fighting'
The Islamists - known as the Union of Islamic Courts (UIC) - swept through Somalia last year, driving warlords out and rapidly extending their influence to much of central and southern Somalia.
Their retreat from Kismayo is seen as a major reversal.
The UIC had withdrawn to the port city on Thursday, after abandoning Mogadishu, which it had controlled since June.
Ethiopian aircraft and artillery are backing Somalia's government
The militia then left Kismayo before a combined Somali-Ethiopian force arrived on Monday.
The BBC's Karen Allen in Nairobi, Kenya, says this is far from the end of the story, as the Islamists have vowed to fight back.
An Islamic commander, Sheikh Yaqub Ishak, confirmed his forces had left Kismayo, but said they would not "stop fighting the Ethiopian invader".
The Islamists have rejected offers of talks with the government, saying Ethiopia must withdraw its forces first.
Ethiopian troops officially entered Somalia on 24 December, joining fighters loyal to Somalia's interim government, to repel an Islamist assault on the government stronghold of Baidoa.
Ethiopia accuses the UIC of harbouring al-Qaeda militants. This is denied by the militia.
The presence of Ethiopian troops on Somali soil could damage the government's attempts to win widespread support, our correspondent says.
The UN estimates that about 30,000 people have been displaced during the fighting, and casualties have been high.