The empty vessels from the Philippines, Vietnam, Malaysia and Myanmar were blown up or scuttled at five separate locations across the country, said Fisheries Minister Susi Pudjiastuti.
The boats had been all caught fishing illegally in the archipelago of more than 17,000 islands. Four Indonesian boats were also sunk after they were caught fishing without proper documentation.
"The government is taking stronger and firmer action to enforce regulations to keep our waters safe," Pudjiastuti, a key figure in the campaign against illegal fishing, told journalists.
However, the campaign has caused tensions with other countries in the region. China last year expressed concern after a Chinese boat was blown up.