In one area the UN estimates 70% of residents need food aid
The US has imposed impossible conditions on aid agencies in Somalia, a UN envoy to the country says.
Humanitarian co-ordinator Mark Bowden said the US was trying to ensure that aid was not diverted to Islamist insurgents fighting the government.
But he said this had politicised their work in a country where hundreds of thousands of people rely on food aid.
Rebels from the hardline al-Shabab group already control much of the capital city and the country's south.
The BBC's East Africa correspondent Peter Greste says the humanitarian crisis has worsened recently amid rumours that a major battle for Mogadishu is about to begin.
About 15,000 people have fled the capital in the past two weeks alone.
Mr Bowden says ordinary civilians are suffering because of a recent US policy aimed at trying to keep food aid away from al-Shabab militants.
"The measures they [the US government] have asked the NGOs and the UN agencies to take - some have been OK and others are seen to be essentially impractical and impossible for us to report on and meet," he said.
He added: "Our concern is that what we're seeing is a politicisation of humanitarian issues.
"And I think that if we can get it back from a political agenda to a more practical humanitarian agenda, we'll all be better off."
The US is Somalia's biggest aid donor - giving $270m (£171m) in 2008, but that figure was almost halved last year.
"We're no longer involved in a discussion about the practicalities of delivering humanitarian assistance with proper safeguards," he said.
"[Now it is] an issue of where assistance can be provided on political grounds."
The US has long accused al-Shabab of being al-Qaeda's proxy in the region.
But the group had denied the links until last month when it released a statement promising to "combine" its local jihad with al-Qaeda's global fight.
Somalia has been wracked by violence for much of the past 20 years. It has not had a functioning central government since 1991.
On Tuesday, the UN said it had opened a new refugee camp in Ethiopia - the fifth camp for Somalis fleeing the violence.
The UN says about 200 Somalis are crossing the border every day.