The murder of Kim Jong-Nam with VX nerve agent at the same airport last month sparked an acrimonious dispute between the two countries.

North Korea has not acknowledged the dead man's identity but has repeatedly criticised the murder investigation and autopsy, accusing Malaysia of conniving with its enemies.

"They have conducted the autopsy without the consent and attendance of the DPRK (North Korea) embassy and later arrested a DPRK citizen without any clear evidence showing his involvement in the incident," ambassador Kang said.

South Korea has blamed the North for the murder, citing what it says was a standing order from leader Kim Jong-Un to kill his exiled half-brother who may have been seen as a potential rival.

Before the ambassador left for the airport, police armed with assault rifles had cordoned off the entrance to North Korea's embassy, with police vehicles and motorcycle outriders parked nearby.

Kang departed in a black chauffeured Jaguar -- the North Korean flag denoting an ambassador now removed from its bonnet. He checked in a Philips TV, three suitcases and four boxes vacuum-wrapped and stamped with the words, DPRK Pyongyang.

Senior government officials told AFP he was expected to leave at 18.25 (1025 GMT) on flight MH360 for Beijing, shortly after the deadline for his expulsion at 1800.

Malaysia declared Kang persona non grata on Saturday and gave him 48 hours to leave the country after he failed to apologise for his criticism of the investigation.

The diplomatic dispute erupted last month when police rejected North Korean diplomats' demands to hand over Kim's body. (AFP)