The Somali government has prevented food aid being distributed in the crisis-hit Lower Shabelle region, international officials have said.
People in the Shabelle region fled flooding as well as the fighting
Two ships carrying aid, which the French navy escorted in to scare off pirates, cannot unload their cargo.
It said it was deeply concerned that the delivery of food aid was being restricted. Ports and airports have been closed and a road convoy halted.
The UN says one million Somalis are homeless because of the fighting.
The head of the national security service said President Abdullahi Yusuf had ordered restrictions to be imposed on the region immediately.
Meanwhile, Mr Yusuf has been taken to hospital in Nairobi. Officials say he is fine but others said he was in a "serious" condition.
He is expected to miss a big meeting on Wednesday in Ethiopia of regional leaders and US Secretary of State Condoleezza Rice.
A spokesman for the UN's World Food Programme said it had not been able to get an explanation - or even confirmation - from the government.
The new rules mean that 3.5 tonnes of food aid which arrived at Marka port under French navy escort to ward off pirates must remain on board.
The WFP also says it has stopped a convoy of trucks bringing food from Mogadishu to Joha after the toll charged at roadblocks rose from $75 to $500 a truck.
No aid agency staff are allowed to move in the region.
The Lower Shabelle, in the south-east, is one of the regions most affected by the growing humanitarian crisis in Somalia.
The Shabelle is sometimes known as Somalia's breadbasket, but severe floods last month worsened an already dire harvest.
The government's order became public a day after a visiting UN official said the international response to the crisis in Somalia had been inadequate.
The humanitarian affairs chief, John Holmes, said aid agencies were having trouble operating because of the poor security situation.
Fighting between Ethiopian-backed government forces and Islamist rebels in the capital, Mogadishu, has forced hundreds of thousands from their homes.
The most recent food aid arrived under French navy escort
The UN refugee agency says 60% of Mogadishu residents have left their homes, including 200,000 this month, following the latest clashes between insurgents and the Ethiopian-backed government.
"This is obviously a very serious humanitarian situation in Somalia," he said, after visiting several camps for displaced people.
A weak African Union force has been unable to stem the violence.
Only 1,600 Ugandan peacekeepers have arrived from a planned 8,000-strong force.
Somalia has not had a functioning national government since President Mohamed Siad Barre was overthrown in 1991.