Under the three-month operation to begin on Sunday, authorities would seek to deport some 500,000 foreigners, mostly from the country's vast and less-developed neighbour Indonesia, Immigration Department Director General Alias Ahmad said.
The operation would involve 135,000 personnel led by the department, he was quoted by The Star newspaper as saying.
Normally laid-back Malaysia has been on edge over dozens of reported shootings, many fatal, that authorities have blamed largely on a gang turf war.
The violence has added to a widespread public perception of rising crime such as thefts, burglaries, and robberies, despite government data showing crime has dropped sharply.
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The figures have been met with wide scepticism.
The national police force, which has endured heavy criticism in recent months as it appeared to be caught unprepared by the shooting spree, launched a separate crackdown on August 17 targeted at gangs.
Police have said 1,400 people suspected of being involved in criminal activity have been detained under that operation.
"It is now time for full enforcement," Alias told The Star. "They can hide, but how long can they hide?"
Alias confirmed the remarks in a text message but he could not be reached for further comment.
Southeast Asia's third-largest economy is a magnet for migrant workers from poorer neighbours Indonesia, Bangladesh, Mynamar, Vietnam, Nepal and elsewhere, who fill low-paid construction, factory and plantation jobs.
Of those, 500,000 have received documents permitting them to work, while 330,000 were repatriated.
The rest have not completed the process, with some workers expressing fear it would lead to deportation as the scheme requires them to be sponsored by a valid employer.