Television footage obtained by Reuters from Japanese media showed Hyon Kwang Song, the second secretary at the North Korean embassy in Kuala Lumpur, and Kim Uk Il, a North Korean state airline employee on the flight from Kuala Lumpur to Beijing.
The Malaysian contingent had been stranded in North Korea amid a protracted spat following the February 13 killing of Kim Jong Nam - the North Korean leader's estranged older half brother - at Kuala Lumpur International Airport.
A van believed to be carrying the body of Kim Jong Nam, the half-brother of North Korea's leader, leaves the forensics wing of a hospital in Kuala Lumpur Thursday.
Police have denied claims that Malaysian authorities confused North Korea for South Korea in the initial investigation into the murder of Kim Jong Nam.
China confirmed that the body had arrived in Pyongyang - after transiting through Beijing - along with "relevant" North Korean nationals.
They say Kim Jong-un had issued a "standing order" for the assassination of his half-brother, in order to consolidate his own power after the death of their father in 2011.
According to Khalid Abu Bakar, the passport found on Kim Jong Nam's body "clearly stated North Korea".
Both objectives were met when three Malaysian diplomats and six family members in Pyongyang returned safely early this morning and the sovereignty of the country was intact, he said.
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But on Friday, in the wake of the larger political deal with North Korea, Mr Khalid said authorities recorded statements from the men and then released them.
Leonid Petrov, a Korea specialist at Australian national university, said he did not expect relations between the countries to suffer in the long term - but suspected North Korea would now be more careful in its covert operations overseas.
Malaysia, however, has officially confirmed his identity using DNA evidence.
Pinkston said that while North Korea could view both the assassination and removing its stranded nationals from Malaysia's jurisdiction as a successful mission, the three men could still likely expect a rough reception at home.
Malaysia will not snap diplomatic ties with North Korea following the row, Malaysian prime minister Najib Razak said during an official visit to India, state news agency Bernama reported.
"We hope they don't create a case like this again", Najib told reporters in the southern city of Chennai.
"Legally, Kim Jong-un is next of kin", he said.
"The next day, the official said it was not Jong Nam, but Kim Chol".