The man, unidentified by police, is one of four people allegedly planning to use the explosives to conduct illegal dynamite or blast fishing.
The outlawed fishing practice destroys coral reef habitats, and kills marine creatures indiscriminately. It can take more than a century before reefs return to normal, according to global anti-illegal fishing report.
A police source said the arrest came after a two-month search.
The three other suspects include two Indonesian citizens and a Timorese person.
The group is detained in Becora detention where they await trial.