The figure of 50,000 IS supporters was based on police intelligence estimates, Transport Minister Liow Tiong said.
About 100 Malaysians have gone to Syria and Iraq to fight with IS and other armed groups, according to police.
Anti-terrorism police have charged more than two dozen IS sympathisers in court.
In November, Malaysia deployed 2,000 soldiers on the streets of Kuala Lumpur after unconfirmed reports of an “imminent terrorist threat” raised alert level.
A police memo, leaked to local media, detailed the presence of at least 10 potential suicide bombers in Kuala Lumpur and eight elsewhere in the country.
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