The report, by the UN's World Food Programme (WFP), says some of the islands have less than two weeks' rice and other essential commodities because the violence has paralysed the distribution system and effectively sealed the islands off from the outside world.
Some 200 people are estimated to have been killed in the violence, but the report reveals a far larger number - 33,000, including children and the elderly - are at risk from food shortages and epidemics.
Police and soldiers opened fire on rioters on the island of Ambon yesterday, following pitched street battles on Wednesday which left at least 12 people dead.
Muslims in Jakarta and on the island of Sulawesi threatened retaliation against Christians and demanded the government brings an end to the killings which haves spun out of control since they began in mid-January.
Stocks of milk on Ambon are exhausted, and the number of ships carrying food have fallen from seven to one or two every week, due to fears among traders that their warehouses will be burned in the riots.
Maluku province, known during Dutch colonial times as the Spice Islands, produces cloves and nutmeg, but has to import most of its rice. In the city of Ambon, the market and 700 shops have been razed, paralysing food distribution.
"The situation is serious," said Thomas Keusters, deputy country director for the WFP in Jakarta. The WFP has appealed for donations from the US and Australian governments, and hopes to receive the go-ahead from the Indonesian government on Monday to begin an aid operation.