News of the deportations was a surprise as the countries have barred each other's citizen from leaving amid a diplomatic standoff over Kim's death.
Malaysian authorities say the estranged half-brother of North Korean leader Kim Jong Un was killed February 13 after two women smeared his face with the banned VX nerve agent at Kuala Lumpur's airport. North Korea widely suspected of being behind the attack rejects the findings.
"As it is kept in the mortuary, the body might decompose, so we did this to preserve the body," he told reporters in Parliament.
Health officials have said Kim's relatives will be given two to three weeks to claim his body before deciding what to do with it.
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North Korea has demanded the body back and objected when Malaysia conducted an autopsy. Pyongyang also has refused to acknowledge that Kim Jong Nam was the victim and has referred to him as Kim Chol, the name on the passport Kim was carrying when he was attacked in a crowded airport terminal.
Relations between the countries have deteriorated sharply since Kim's death, with each expelling the other's ambassador.
Last Tuesday, North Korea blocked all Malaysians from leaving the country until a "fair settlement" of the case was reached. Malaysia then barred North Koreans from exiting its soil.
Zahid, who earlier said negotiations were ongoing, said today that about 50 North Koreans detained in eastern Sarawak state for overstaying their work permits will be sent back to Pyongyang soon. He didn't give details nor say why they would be deported amid the exit ban.
Although Malaysia has never directly accused North Korea of being behind the attack, many speculate that Pyongyang must have orchestrated it.
Experts say the VX nerve agent used to kill Kim was almost certainly produced in a sophisticated state weapons laboratory, and North Korea is widely believed to possess large quantities of chemical weapon.
Four of the seven North Korean suspects being sought by Malaysia are believed to have left the country the day Kim was killed. Police say the other three, including a North Korean diplomat, are believed to be in the North Korean Embassy in Kuala Lumpur.
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