The ship left the port of Colombo late Tuesday under the Red Cross flag with aid for some 350,000 people cut off in the northern district by clashes between separatist Tamil rebels and government forces.
"The boat left last night with about 1,500 tonnes of food and 15 tonnes of medical supplies," said World Food Programme country director Jeff Taft-Dick.
An offensive by separatist Tamil Tiger rebels launched 12 days ago, which the military said was aimed at capturing Jaffna, has cut off all road access to the area and more than 40,000 people have fled their homes.
Military officials said there was a lull in fighting in the Jaffna peninsula in the past three days with the exception of an air raid on a suspected Tiger ammunition dump on Tuesday.
Aid agencies planned to load the ship with 2,600 tonnes of food but heavy rains repeatedly halted loading of the boat, which had been due to leave over the weekend.
Government workers warned that food would run out on Thursday in the besieged zo