An MSF spokesman said food was having to be distributed to more than 70,000 people in the area displaced by the sectarian clashes which have killed hundreds in the Moluccan islands this year.
Less than half - about 30,000 - were in refugee camps and some of the refugees had been without proper homes for a year, he added.
Sectarian violence in the region is centred on Maluku - a small province with only two million people where the two main religious groupings are equally balanced.
Thousands of houses have been destroyed in the violence and tens of thousands of people have fled to other Indonesian regions.
MSF is one of the few international aid agencies still working in the area.
President's plea for peace
Despite the presence of a large troop contingent, the province is now effectively segregated along religious lines with neighbourhoods and villages have becoming barricaded, armed camps.
Sectarian clashes have continued despite a plea for peace from Indonesian President, Abdurrahman Wahid who visited the region last week.
The official Indonesian news agency Antara said that three people were killed in renewed violence in the Moluccan Islands, shortly after the president's visit.
President Wahid urged Muslims and Christians to end the clashes or face intervention from the government.
People must regain respect for each other," Mr Wahid said.
"This is not just a problem for this region. It is a national issue."
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