The passenger list was not immediately available but agency representatives said aid workers and United Nations staff were on board. There were three crew members on the flight.
Teams searching for the ATR-24 transport aircraft found the wreckage in a heavily mined area near the village of Slakovce, a UN official said.
A WFP spokesman said it was not known if there were any survivors, because fog was hampering the rescue attempt. Catherine Bertini, the WFP chief, said the agency had no idea what caused the crash. The aircraft left Rome at 9.05am and entered Macedonian air space at 10.50am. The last radio contact with the plane was at 11.15am. It was about 10 miles north of Pristina when it disappeared from radar screens.
Helicopters with the Nato-led K-For intervention force in the Serbian province led the search for the plane, which disappeared from radar screens at 12.13pm, 10 miles north of the Kosovo capital.
Catherine Bertini, executive director of the WFP, said: "K-For have not been able to get to the site yet to check on the passengers. We have no idea what happened."
She said no details about the passengers would be released until all next-of-kin had been contacted. The WFP is responsible for supplying food aid to about 900,000 people in Kosovo.