Police said the other three men are believed to be hiding in the North Korean Embassy in Kuala Lumpur.
Kim Jong Nam, the half-brother of the North's leader Kim Jong Un, was murdered at Kuala Lumpur's airport on February 13 in a freakish assassination using toxic nerve agent, sparking a row between the two countries that had friendly relations before.
On Thursday, Najib said a deal had been struck - Kim Jong Nam's body had been released to North Korea and the nine Malaysians had been allowed to board a plane home.
Malaysian prosecutors have charged two women - an Indonesian and a Vietnamese - with killing him, but South Korean and United States officials had regarded them as pawns in an operation carried out by North Korean agents.
"(North Korea) got all that it wanted - the body, especially the release and safe passage of the North Korean (s)", named in relation to the killing, Razali said.
"The effect had to be planned", said Robert Gallucci, a former USA chief negotiator with North Korea over its nuclear program.
But the North denies this and denounced Malaysia's investigation into the death as an attempt to smear the secretive regime.
The nine Malaysian nationals were met by their relatives and a large media contingent at Kuala Lumpur airport early on Friday.
Malaysian Prime Minister Najib Razak initially announced a tit-for-tat ban, accusing North Korea of "effectively holding our citizens hostage".
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They were flown home in a business jet plane piloted by members of the Malaysian air force.
The deal largely ended a diplomatic battle that had also left more than 300 North Koreans stranded in Malaysia, but left questions about the status of Malaysia's investigation into the death of Kim, the half brother of North Korean leader Kim Jong Un.
Mohamad Nor Azrin, the counselor of the Malaysian Embassy in North Korea, said all of the Malaysians who were stuck North Korea were allowed to move around and were not threatened while in Pyongyang.
As tensions escalated in recent weeks, both countries withdrew their ambassadors and North Korea blocked nine Malaysians who were in the country at the time from leaving. Earlier, sources told Reuters authorities were preparing to transport Kim's body on Malaysia Airlines flight MH360 to Beijing. The two an Indonesian and a Vietnamese say they were duped into thinking they were taking part in a hidden-camera prank TV show.
North Korea does not even acknowledge the victim is Mr Kim, referring to him instead as Kim Chol, the name on the passport he was carrying when he died. When asked if this meant that the North Korean leader had written the letter which had secured the body's release, the IGP replied: "You said it, not me".
North Korea had demanded custody of the body because the victim was one of its citizens.
Mr Kim's own family previously lived in Macau but they are now thought to be in hiding.
Eight North Koreans have also been identified as suspects or persons of interest by Malaysian authorities.