"They took off from Pyongyang today at 7:45 pm (1145 GMT) Malaysian time, and will land in Kuala Lumpur tomorrow around 5:00 am", he said in the statement that referred to Kim Jong-Nam as "the deceased" rather than by name.
The Malaysian government has ordered the body of Kim Jong-nam to be returned to North Korea.
The tension between Malaysia and North Korea arose in the wake of the murder of Kim Jong-nam, elder half-brother of North Korean leader Kim Jong-un, in Malaysia on Feb 13.
North Korea and Malaysia's historically close ties began to unravel in the wake of Kim's death, hitting a nadir when Pyongyang banned nine Malaysian citizens from leaving the country in retaliation for the Kim investigation.
Prime Minister Najib Razak said late Wednesday that negotiations were "very sensitive" to ensure the safety of nine Malaysians - three embassy staff and six family members - who are stranded in North Korea's capital.
Malaysian police say Kim was killed on February 13 by two women who smeared super toxic VX nerve agent on his face at the Kuala Lumpur budget terminal.
Malaysian investigators have demanded that North Korea hand over the suspects of the killing.
Soon, both countries had expelled the others' ambassadors.
John McCain has managed to infuriate North Korea after criticizing both Kim Jong-un's politics and physique in one scathing crazy fat kid insult.
North Korea says it tested rocket engine 'of historic significance'
Claiming the test to be successful, Kim Jong-un said it was a new birth of the nation's rocket industry. After the test last April, North Korea's rhetoric was much more intense.
South Korea has blamed Pyongyang for the killing, citing what they say was a standing order from Kim Jong-Un to kill his exiled half-brother.
Amidst tears of joy, Defense Advisor of Malaysian Consulate in North Korea, Mohd Nor Azrin Md Zain and wife, Iza Karmila Ramli along with their children, Annur Zuaikha, Aynur Zhafirah and Ayscha Zinnirah looked joyous to be home.
"I have instructed for all possible measures to be taken to bring those responsible for this murder to justice", Najib added.
- March 1: Indonesian Siti Aisyah, 25, and Doan Thi Huong, 28, from Vietnam are charged with murder. Authorities also say they are looking for seven North Koreans.
McCain didn't mince his words when referring to Kim during an interview with MSNBC last week, stating that "China is the only one that can control Kim Jong-un, this insane fat kid thats running North Korea".
North Korea reacted angrily when the Malaysian authorities identified North Korean suspects and sought to question others including a diplomat at their embassy in Kuala Lumpur.
Kim, who was in his mid-40s and had lived overseas for years, was estranged from his younger brother, North Korean leader Kim Jong Un.
Another "important" but unnamed North Korean national is also being sought, Malaysian police inspector-general Khalid Abu Bakar said last week.
Malaysia's Prime Minister Najib Razak initially announced a tit-for-tat ban, accusing North Korea of "effectively holding our citizens hostage".