Commodore Rufino Lopez Jr., chief of the Naval Forces Western Mindanao, said several naval units have been sent to the islands of Tawi-Tawi following reports that the pirates took their hostages to one of the islands in the area.
"Our naval units are checking the islands," Lopez said.
"We have sent our task force there who are presently checking the islands of Sibuto and Sitangkai where the suspects (are) believed to have brought their captives."
The Navy identified the three Indonesian hostages as tugboat captain Ahmad Rumiyati, 33, Yamin Labusu and Erekson Hutagul.
They were seized when five gun-wielding pirates boarded their vessel, the Bonggaya 91 tugboat, off Malaysias Sabah state on Wednesday.
Initial reports said Filipino pirates boarded the boat in Malaysian waters off Semporna in the eastern state of Sabah on Borneo island before fleeing towards Tawi-Tawi archipelago.
Lopez said their initial investigation indicated the attackers were Filipino pirates.
Navy spokesman Capt. Geronimo Malabanan said the Philippine Navy is coordinating with the Malaysian police over the kidnapping incident.
The Bonggaya 91 was on its way back to Sandakan in Sabah from Indonesia when it was attacked and boarded Wednesday morning.
Lopez said the pirates, piloting a speedboat and armed with M-16 and AK-47 rifles, intercepted the slow-moving tugboat near Mataking island, near Palau off Semporna east of Sabah.
The gunmen fired warning shots as they jumped aboard the tugboat and seized three of the six crewmen. They then ripped out the ships communication equipment before escaping towards the southern Philippines border with the hostages.
The remaining crewmembers arrived in Sandakan yesterday.
The pirates seized the boats radio communication set and mobile phones, said Chang, director of Syarikat Pengangkutan Bonggaya.
"Luckily one of my crew hid his mobile phone and was able to call me," he said.
"He (one crew member) said they had been attacked by the Abu Sayyaf. We have no idea how true this is. I immediately notified the police."
Authorities believe the abduction may be the work of the Abu Sayyaf.
Last year, Abu Sayyaf kidnappers seized three seamen two Malaysians and an Indonesian who were discovered early this year to have died in captivity.
The bandit group also seized 21 Western tourists and Malaysian and Filipino resort workers from Sipadan in Malaysia in 2000. Most of the hostages were freed after ransom was paid.
Last Wednesdays abduction followed the kidnapping of two Japanese and a Filipino who were snatched from a Japanese-registered tugboat while sailing along the pirate-laden Strait of Malacca. They were released last March 21. Jaime Laude, AFP