"The situation is dire for hundreds of thousands of people who have lost their homes, their belongings and most of their crops," World Food Programme chief Josette Sheeran said in a statement.
Uganda was one of the countries most affected by the torrential rains and floods that have swept much of sub-Saharan Africa in recent weeks.
Northeastern regions of Uganda were devastated by the worst floods in decades, with some 300,000 people either displaced or deprived of their crops, according to the WFP.
"WFP needs 17 million dollars (12 million euros) to buy food for flood victims and 3.2 million dollars to provide trucks, boats, aircraft and emergency road and bridge repairs on behalf of the humanitarian community," the statement said.
The agency said it needed a total of 60 million dollars for its humanitarian operations in Uganda, stressing it had only received a fifth of the sum so far and that its funds were already depleted prior to the floods.
"We are quickly running out of food, and before long, thousands of flood-hit families will have nothing else to eat," Sheeran said.
"Without new contributions, WFP's food assistance supply line for a total of 1.7 million people in Uganda will break in December," the statement said.
At least 300 people in 20 countries have died in floods over the past two months, according to figures from governments, hospitals and humanitarian sources compiled by AFP.