Al Jazeera aired a program showcasing the country’s treatment of undocumented foreign workers during the coronavirus pandemic.
The show entitled “Locked Up in Malaysia’s Lockdown” aired on July 3, but was met with backlash in the country.
Malaysian authorities brand the report as inaccurate, misleading, and unfair.
Rights groups have accused the government of suppressing media freedom after Al Jazeera journalists were called in for questioning by the police.
An investigation was opened into alleged sedition, defamation, and violation of a communications law.
Malaysian police seized two computers from the Al Jazeera office during Tuesday's raid, the Qatar-based broadcaster said in a statement.
"Conducting a raid on our office and seizing computers is a troubling escalation in the authorities' crackdown on media freedom and shows the lengths they are prepared to take to try to intimidate journalists," Al Jazeera said.
Al Jazeera said it stood by its report and called on authorities to drop the criminal investigation.
Malaysian police did not immediately respond to a request for comment.
Malaysia arrested hundreds of undocumented foreigners, including children and Rohingya refugees, after the country imposed a lockdown to contain the spread of the new coronavirus.
Human rights activists have condemned the arrests as inhumane.
Malaysian officials have said they were necessary to prevent the spread of the virus.
Activists have voiced concern that the five-month-old administration of Prime Minister Muhyiddin Yassin is stifling dissent amid a series of clampdowns, an accusation it has denied.
Last month, authorities arrested a Bangladeshi man who criticized the government's treatment of migrant workers in the Al Jazeera program.
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