Head of the criminal section of the Sorong prosecution office Danang P Dwiharjo in Sorong said the two boats would be exploded if the court gave the guilty verdict.
The two boats are now detained at the fishing terminal of Sorong and their cases are being processed by the prosecution office, Danang said.
The two boats with skippers Graciano Maglasang (51) and Rodrigo Puno (48) and 47 crew members were caught by Indonesian sea security authorities off Raja Ampat on Wednesday.
Danang said the boats were caught with 3 tons of tuna fishes worth around Rp500 million.
He said the two Philippines skippers claimed they were not aware that they had entered Indonesian water territory.