The UN envoy for recovery, relief and reconstruction, Nigel Fisher, said the World Bank trust fund for Afghanistan's interim administration had received only $45m of the $400m (£275m) budget needed to run the government.
About $4.5bn in aid over five years was pledged at a donors' conference in Tokyo in January, after the Taliban were bombed out of power by US-led forces.
Overall, the UN requested $1.8bn for Afghanistan between October 2001 and December 2002 but only $870m had been paid, Mr Fisher said.
The $526m received after the Afghan donor conference in Tokyo fell "well below aspirations", he said.
'Not enough'
"We face the fact that overall what is coming into this country is insufficient and will continue to be so whatever is being done," Mr Fisher said.
Mr Fisher denied the UN had underestimated how much money would be needed to reconstruct Afghanistan.
"It's a question of too little perhaps is offered," he said.
Mr Fisher said even 10 times the amount pledged would not be enough to repair the damage from 23 years of war, prevent hunger, and house hundreds of thousands of returning refugees.
Food shortage
The International Organisation of Migration, which has repatriated over 250,000 people, on Sunday indefinitely suspended transport for returning refugees due to lack of funds.
The UN's World Food Programme, which is feeding nine million Afghans facing starvation after years of drought, has also run short of food.
"We still have an immediate humanitarian crisis facing us," said Mr Fisher.
"Priorities mean some people, some communities, some parts of the country get resources, it means others are left out," he said.
Food assistance to civil servants, designed to keep the government running smoothly, may be cut back in coming weeks, he said.