More than three weeks of fighting between the army and Tamil Tiger fighters has forced 180,000 people to flee their homes and created a humanitarian crisis in north and east Sri Lanka.
With road links cut and sea and air links limited, shortages are rife.
Air strikes and artillery continued in parts of the region on Friday. Diplomats say Sri Lanka's two-decade civil war between government forces and the Liberation Tigers of Tamil Eelam (LTTE) has now effectively resumed, and returning to a 2002 ceasefire seems unlikely unless both make concessions.
A Reuters witness saw the ship anchored off the jetty at Point Pedro, on the northern edge of the Jaffna peninsula, as several barges that survived the 2004 tsunami began to ferry ashore around 1,500 tonnes of food for Jaffna residents.
Officials said the ship would sail north out of the conflict area before nightfall, anchor and then return the next day to continue unloading.
Most shops on the Jaffna peninsula have run out of food and some of its half-million people are down to one meal a day. For the last few days, the military has relaxed a curfew and allowed people out for five hours a day.
Rajini Vethanayagam, a 40-year-old mother of three, said: "But what can we achieve in those five hours?
"Nothing. Just wait in queues. Everywhere is very overcrowded, prices are high and most of the goods are not available."
The United Nations world food programme - already providing food to an estimated 200,000 people displaced by the fighting - said it was also worried about rising shortages in Tiger-held areas of the north and east, with border crossing points shut and aid agency access sometimes blocked by the military.
Jeff Taff-Dick, the WFP country director, said: "Without better access, WFP will not be able to continue feeding displaced persons living in areas outside of government control."
He also said that high level meetings between the UN and the government had not solved the issue.
Another small ferry flying the Red Cross flag sailed from the northeastern port of Trincomalee on Friday morning to evacuate the first 150 of an estimated 500 expatriates from Jaffna - mainly ethnic Jaffna Tamils with British or Canadian passports.
The Red Cross said that with security guarantees from both sides, they were confident their neutrality would be respected.