At least 33 people were rescued after the accident 40 miles off the coast of Prigi in East Java province on Saturday, search officer Iwan Rosadi said in the provincial capital Surabaya.
Marine police and local rescue personnel were searching the water while helicopters conducted an aerial surveillance, but rough seas were hampering the efforts, officials said.
About 250 people, including undocumented migrants from Iran, Afghanistan and Iraq were believed to have been on board, local rescue official Edwin Purnama said.
"Survivors said the boat had engine trouble and leaked after it was hit by strong waves," Purnama said by telephone.
Search coordinator Kelik Purwanto said hopes of finding more survivors were small.
"There's a slight chance that some of them may have stranded on small islands," he said.//DPA