Musa Aman, the chief minister of Sabah state, said Manila was not cooperating in accepting its nationals back, the state Bernama news agency reported.
"What I want to say here is that we will continue to round up the illegal immigrants in Sabah to ensure they are sent back to their home countries," Musa was quoted as saying.
"However, to repatriate them all is not easy because some countries, particularly the Philippines, have failed to give decent cooperation, causing the process to send their nationals back to take a very long time," he said.
Sabah shares a border with Indonesia and is separated by the narrow Sulu Sea from the Mindanao region in the southern Philippines, which shares cultural ties with Sabah.
Officials say there are up to half a million illegals living in Sabah  mainly Muslim Filipinos and Indonesians who are engaged in local industries such as fishing, plantation and construction.
Malaysia has launched a number of mass deportations, and in June last year held high-level talks with the Philippines over what both sides said was the growing problem of Filipino migration.
"Police in all districts have carried out operations almost every day to trace and round up the illegal immigrants and hold them at the detention centers pending repatriation," Musa said.
But Patrick Sindu, president of the Consumers Association of Sabah, went further Wednesday, saying that the problem was "very serious" and accused many illegals of criminal activities such as robbery and rape.
"It is clear the Malaysia government has no political will to solve the illegal problem," he said.