A 46-year-old was arrested on Friday evening with documents that identified him as North Korean citizen Ri Jong Chol, a police statement said, making him the first person from the North to be detained over the case.
Kim Jong-Nam died after an as-yet unidentified liquid was sprayed in his face at Kuala Lumpur international airport on Monday, in an attack Seoul says was carried out by female agents from Pyongyang.
Jong-Nam's body has been held in a Kuala Lumpur morgue since an autopsy on Wednesday, the results of which are still pending, according to Selangor state police chief Abdul Samah Mat.
After Malaysia ignored demands to return the remains, Pyongyang accused the Kuala Lumpur of conspiring with its enemies and said it would reject whatever results came from the post-mortem.
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"The Malaysian side forced the post-mortem without our permission and witnessing. We will categorically reject the result of the post-mortem conducted unilaterally excluding our attendance," the North Korean ambassador told reporters gathered outside the morgue shortly before midnight on Friday.
North Korean state media has remained silent on the murder.
The ambassador had met with Malaysian police, demanding the release of the body without success, according to an English transcript of the envoy's comments distributed by an aide.
"They are colluding with the hostile forces towards us who are desperate to harm us of malice," the transcript said, suggesting South Korea was trying to defame the North in a bid to distract from a corruption scandal at home.
"While in Malaysia, everyone has to obey and follow our rules and regulations... That includes North Korea," Inspector-General of Police Tan Sri Khalid Abu Bakar told national news agency Bernama.