Indonesia on Monday freed a Singapore-flagged vessel captured by pirates off the coast of Borneo island, and detained nine suspects involved in the hijacking, a navy spokesman said.

The 20 crew and one passenger who were aboard the captured boat were unharmed during the operation, navy spokesman Edi Sucipto said in a statement.

The vessel had disappeared from radar inside Indonesian waters before reappearing some distance away under a different name, arousing suspicion.

Sucipto said the navy pursued the vessel before securing it and freeing the captive crew.

The pirates had planned to shift 200 kilolitres of oil from the Singapore-flagged ship to another vessel, he added.

Nine Indonesian citizens were detained on suspicion of piracy and were being transferred to Surabaya city, on northeastern Java island, for further questioning.

Piracy is not uncommon along Southeast Asia's lucrative maritime trade routes.

Indonesia has vowed to protect its vast archipelago from illegal incursions by unregulated fishers and pirates, and has seized hundreds of vessels in a tough crackdown.

"The Indonesian navy will continue to patrol the seas to maintain safety within Indonesian territory," Sucipto said.