The employees, three men from each country, were seized late on Sunday in a raid on the Borneo Paradise Resort on the River Sabahan in eastern Sabah state, said Malaysian police chief Norian Mai on Monday.
Sabah borders the Philippines’ troubled region, and resorts in the state were targeted by rebel Philippine groups twice in 2000.
Some of the 10 kidnappers wore military fatigues and carried modern weapons, said Norian. He ruled out speculation that the Philippine rebel group Abu Sayyaf was responsible.
Abu Sayyaf kidnapped 21 people, mainly Western tourists, from the Sipadan resort in Sabah in April 2000, holding them for nearly a year before releasing them, reportedly in exchange for millions of dollars in ransom.
Norian said the Philippine group had been ruled out because of the target - workers rather than foreign tourists. The police chief said the main suspects were likely locals seeking ransom.
Indonesian and Philippine armed forces are cooperating in the search for the kidnappers, said Norian.
The resort is about 2km from the coast and 38km from the nearest town Kunak. It has just 15 rooms, catering mainly for local tourists and campsites for schoolchildren outings.
The kidnappers have not communicated with the authorities, said Norian.