Ethiopian aircraft and artillery are backing Somalia's government
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Kenya has beefed up its security and closed its border with Somalia to halt defeated Islamic militias driven from Kismayo in southern Somalia.
The Islamists say their retreat from advancing Ethiopian and Somali forces is tactical and warns of an insurgency.
A BBC reporter says helicopters and hundreds of army and police have deployed in the border town of Luboi.
The BBC's Bashkas Jugsodaay says a lot of Somali refugees are stranded at the border and are in a bad way.
Somalia's interim President Abdullahi Yusuf is meeting Kenyan leader Mwai Kibaki in Mombasa to discuss security.
The two-week advance of heavily armed Ethiopian forces ended a six-month Islamist occupation which had brought a degree of stability to large areas of formerly lawless Somalia.
Border
Ten fighters arrested trying to get into Kenya at the weekend were foreigners backing the Islamists, according to Somali's interim government.
The United Nations Humanitarian co-ordinator for Somalia, Eric La Roche, has expressed concern at the border closure saying it would affect women and children.
Medical aid agency, Medicines sans Frontiers (MSF) plans to send its international staff back into Somalia this week if provided with adequate guarantees. It pulled its international staff out of Somalia two weeks ago.
Two top Islamist leaders are reported to have been seen south of Kismayo with dozens of armed pick-up trucks following their retreat from Kismayo. Ethiopian forces are said to be in pursuit.
Ethiopian forces are set to remain in Somalia to ensure stability after the defeat of Islamist militias, but splits have emerged over when they may leave.
Ethiopian Prime Minister Meles Zenawi told MPs that he hoped his forces could withdraw within two weeks.
But the prime minister of Somalia's fragile interim government, Ali Mohamed Ghedi, says that heavily-armed soldiers from Ethiopia would be needed for months.
Divisions
Somalia's weak interim government wants Ethiopian forces to remain in the country until peacekeepers deploy, as they have few well-trained troops and are poorly placed to maintain law and order without help.
The only solution in Somalia is sincerity of all the stakeholders 
But the presence of Ethiopian troops on Somali soil could also damage the government's attempts to win widespread support, the BBC's Karen Allen says.
As if to illustrate the divisions, the deputy prime minister in Somalia's transitional government, Husayn Aideed, has been criticised by the prime minister's spokesman after calling for unity with Ethiopia.
Speaking to clan leaders in Mogadishu, Mr Aideed said the two countries should follow the example set by Europe which was divided by two world wars and now was united.
"We share a 2,000km long border. We are brothers. There is nothing that divides us. We want one passport. One army. One security. One economy."
But Abdirahman Dinari said this was definitely not government policy.
On Monday, Mr Ghedi set a deadline of Thursday for all Somalis to hand in their weapons, but this has reportedly borne little fruit so far in the capital, Mogadishu.
He has also offered an amnesty to fleeing Islamists if they give themselves up.
European members of the Somali Contact group are due to meet in Brussels on Wednesday to discuss how Europe can help peace efforts in Somalia.
