Twelve of the boats will be blown up and sunk this month, said Fuad Himawan, the head of enforcement at the Fisheries and Marine Resources Ministry.
The 39 boats were seized from Vietnamese, Malaysian and Thai fishing crews, he said.
Last year, Indonesia sank more than 100 foreign boats for fish poaching.
Fisheries Minister Susi Pudjiastuti has taken a tough stance against illegal fishing, saying she will continue to blow up vessels operated by foreign poachers.
She has said Indonesia loses 15 billion dollars every year to illegal fishing.
DPA