The World Food Programme (WFP) said it could have to close parts of its airway, used to fly aid workers to humanitarian trouble-spots.
Deliveries have already been suspended to north Uganda, Ivory Coast and Niger.
The UN Humanitarian Air Service (UNHAS), operated by WFP, has a budget for 2009 of $160m (£96m) but has received less than $90m in fees and contributions this year.
WFP spokesman Greg Barrow said UNHAS was “a vital component of humanitarian operations across the world”.
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Pierre Carrasse, Chief of WFP’s Aviation Branch, asked how workers could reach the often remote areas affected by conflict without the airline.
“How will WFP reach the hungry? How will doctors reach their patients? How will people have clean water if the engineers who help to build wells can’t get there,” he asked.