The authorities will conduct raids mainly in Kuala Lumpur, Selangor, Penang and Johor, which have been identified as the dens for illegal immigrants.
The Immigration Department is the lead agency of the programme.
The operation will also involve some 135,000 personnel from the Immigration Department, police, Armed Forces, Rela (a paramilitary civil volunteer corps), Civil Defence, National Registration Department and local councils.
Malaysia relies heavily on foreign labour sourcing from India, Indonesia, Bangladesh, Vietnam, Nepal and Myanmar.
Employers found hiring illegals could be charged under the Anti-Trafficking in Persons and Smuggling of Migrants Act, local media reports said.
Immigration director-general Alias Ahmad said the department would seek the cooperation of foreign missions through the foreign ministry to issue illegal immigrants with travelling documents to speed up their deportation.
The operation is targeted at people who registered under the Illegal Immigrant Comprehensive Settlement Programme but did not turn up for further processing, including legalisation and voluntary deportation, Ahmad was quoted as saying by The Star.
Of the registered people, 500,000 applications for legalisation were processed while 330,000 were repatriated.
"We have given them more than a year to take up the offer. It is now time for full enforcement," Ahmad said, adding that the majority of the targets were Indonesians.
Other targets of the programme included, Bangladeshis, Myanmar nationals, Vietnamese and Nepalese.
Ahmad said the operation would be like "a cat and mouse" game, but "we are fully prepared for it".
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