Kim Jong-Nam, 45, was poisoned on February 13 at Kuala Lumpur International Airport with VX, a nerve agent so deadly that it is classed as a weapon of mass destruction.
The dramatic killing has sharply soured relations between Malaysia and North Korea, which has not acknowledged the dead man's identity, vehemently protested the murder investigation and accused Kuala Lumpur of being in cahoots with its enemies.
Arch-rival South Korea has blamed the North for the murder, citing what they say was a standing order from leader Kim Jong-Un to kill his exiled half-brother who may have been seen as a potential rival.
"The ambassador has been declared persona non grata" after Malaysia demanded but did not receive an apology over Pyongyang's attack on its investigation of the case, the statement added.
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"He is expected to leave Malaysia within 48 hours."
The row erupted last month when Malaysian police rejected North Korean diplomats' demands to hand over Kim's body.
Ambassador Kang Chol reacted by saying that the investigation was politically motivated and that Kuala Lumpur was conspiring with "hostile forces".
Malaysia also recalled its envoy to Pyongyang and has cancelled a rare visa-free travel deal with North Korea, putting the skids under once cozy ties.
The rift widened on Thursday when a senior North Korean diplomat leading a delegation to Kuala Lumpur reiterated Pyongyang's assertion that Kim had died of a heart attack, dismissing the use of a nerve agent.
The foreign ministry statement said that on February 28 the government had already issued Pyongyang a same-day deadline for a written apology over Kang's accusations.
Kang's expulsion order came the same day that the only North Korean arrested over the assassination denounced Malaysia's probe as "a conspiracy to impair the dignity of the Republic (North Korea)".
Ri Jong-Chol, who was released and deported yesterday due to lack of evidence, said that police had offered him a comfortable life in Malaysia in return for a false confession.
Ri's release came days after two women -- one Vietnamese and one Indonesian -- were charged with murdering Kim Jong-Nam.
Police say he suffered a seizure and died less than 20 minutes later. Swabs of the dead man's face revealed traces of VX nerve agent.