Prime Minister Najib Razak said a coroner had approved the release of Kim Jong-nam's body.
Mr Kim was murdered at Kuala Lumpur airport with a lethal nerve agent last month.
The assassination led to a major diplomatic dispute between Malaysia and North Korea.
Malaysia has not directly blamed North Korea for the killing, but there is widespread suspicion that Pyongyang was responsible.
Meanwhile, nine Malaysians who had been barred from leaving North Korea returned to Malaysia early on Friday. They include three embassy staff and six family members.
Prime Minister Najib had also said that all North Koreans would be allowed to leave Malaysia.
BBC South East Asia correspondent Jonathan Head says that probably includes three North Koreans who are wanted by Malaysian police in connection with the killing.
Malaysia expressed outrage earlier this month over what it described as North Korea holding its citizens hostage. But now it appears to have acceded to North Korea's wishes to get those Malaysians released, our correspondent adds.
A video circulated by Japanese media later on Thursday reportedly showed two of the suspects - an embassy employee and a worker for the North Korean state airline - on a plane, and cargo said to be Mr Kim's casket.
Mr Najib said: "I had a deep personal concern about this matter, and we worked intensively behind the scenes to achieve this successful outcome.
"Many challenges were overcome to ensure the return of our fellow Malaysians."
He added: "The government believes strongly in the principles of justice and sovereignty. Our police investigation into this serious crime on Malaysian soil will continue.
"I have instructed for all possible measures to be taken to bring those responsible for this murder to justice."
Two women - one Vietnamese woman and one Indonesian - have been charged with killing Mr Kim. Both reportedly believed they were participating in a television prank.
CCTV footage shows the two approach Mr Kim as he waited for a flight and smear VX nerve agent on his face. He died within 20 minutes.
Interpol has issued a "red notice" for four North Koreans wanted in connection with the assassination.
Malaysia said the four men were at the airport on the day Mr Kim was killed and had since left the country. They are thought to be in North Korea.
A red notice is the nearest equivalent to an international arrest warrant. The move is unlikely to result in arrests as North Korea is not a member of Interpol.
The four named in the Interpol red notice are Ri Ji Hyon, 33, Hong Song Hac, 34, O Jong Gil, 55, and Ri Jae Nam, 57.
Kim Jong-nam, who was the estranged, elder half-brother of Kim Jong-un, had been passed over for the North Korean succession and was living in the Chinese territory of Macau at the time of his death.
It is not clear where Mr Kim's wife and children are, although his son appeared in a video earlier in March and said the family were together.