Malaysian police investigating what US and South Korean officials say it was an assassination carried out by North Korean agents took statements from the three before they were allowed to leave the country.
The BBC News said the North Korean government was suspected of orchestrating the death against the late Kim Jong Ill's oldest son.
The mutual release ends the two nations' travel bans on each others' nationals, a development that came after weeks of disagreement over the death of Kim Jong-nam.
Mohd Nor Azrin, a Malaysian diplomat who was detained with this wife and three children in North Korea, expressed his relief upon arrival.
Malaysian police investigating what US and South Korean officials say was an assassination carried out by North Korean agents at Kuala Lumpur's airport took statements from the three suspects before they were allowed to leave the country.
"In the beginning we said we would like them to assist in the investigation and we have allowed them to go", Khalid told a news conference in Kuala Lumpur.
The other North Koreans named by Malaysian investigators are all back in North Korea.
North Korea has maintained that the dead man is not Kim Jong-Nam, saying instead the body is that of Kim Chol, the name on the victim's passport.
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China's foreign ministry spokesperson Lu Kang told a media briefing that Beijing "offered necessary assistance to the transit of the body".
The tense diplomatic relations between Malaysia and North Korea eased slightly in the last two months when the nine Malaysian nationals, who were earlier prohibited from leaving North Korea following the diplomatic tiff between Kuala Lumpur and Pyongyang, arrived here safely this morning.
South Korea has blamed the north for the brazen killing, citing what they say was a standing order from Kim Jong-un to murder his exiled and estranged half-brother. It had insisted that the man, who it has not named, died of a heart attack.
Two women - an Indonesian and a Vietnamese national - have been charged with killing Kim Jong-Nam, but claim they believed they were involved in a prank. Airport CCTV footage shows them approaching Kim Jong-nam and apparently smearing his face with a piece of cloth.
Malaysian Prime Minister Najib Razak described the outcome as "successful", and said he and his staff had "worked intensively behind the scenes" to resolve the issue.
"Following the completion of the autopsy on the deceased and receipt of a letter from his family requesting the remains be returned to North Korea, the coroner has approved the release of the body", Mr Najib said, adding that the murder investigation would continue but the travel ban on North Koreans would be lifted.
Malaysian police had previously said two female suspects, one Indonesian and one Vietnamese, together with four DPRK suspects, carried out the February 13 attack on the DPRK man at the airport.