Malaysia has unleashed airstrikes and mortar attacks on nearly 200 Filipinos occupying a Borneo coastal village.
However, it could not declare an immediate end to a three-week siege that has turned into a security nightmare for both Malaysia and the Philippines.
The assault follows clashes this past week that killed eight Malaysian police officers and 19 Filipino gunmen.
Malaysia and the Philippines were shocked when a Muslim clan slipped past naval patrols last month and stormed the obscure village in Borneo's eastern Sabah state.
The armed group had refused to leave the area, staking a long-dormant claim to Malaysia's entire state of Sabah, which they insist is their ancestral birthright.
The crisis has sparked worries of a spread of instability in Sabah, which is rich in timber and oil resources.
Other armed Filipinos are feared to have slipped into other districts in the area recently.
Many hours after fighter jets were deployed, national police chief Ismail Omar said police and military personnel were still hunting for Filipinos in an area of about 4sq.km.
"We believe there are still enemies in the area," Mr Ismail said.
Prime Minister Najib Razak defended the offensive.
He said Malaysia had made every effort to resolve the siege peacefully since the group's presence in Lahad Datu district became known on 12 February.
"For our sovereignty and stability, we will not allow even an inch of Malaysian territory to be threatened or taken by anyone," Mr Najib said.
The Filipinos who landed in Lahad Datu, a short boat ride from the southern Philippines, say Sabah belonged to their royal sultanate for more than a century.
Abraham Idjirani, a spokesman for the Filipinos, told reporters in Manila that the group would not surrender and that their leader was safe.
Malaysian officials said they were taking no chances with public safety, sealing off areas within about 30km of the village and refusing entry to journalists.
The Philippine government had urged Malaysia to exercise maximum tolerance to avoid further bloodshed.