He died 20 minutes later.
The Deputy Prime Minister said there were a total of 315 North Koreans in Malaysia, adding that negotiations are ongoing with North Korea to allow the remaining nine Malaysians there to return.
He said: "Now with the positive identification of the body, we are told that he had a wife or wives and children".
The body was secretly taken out of the morgue for the embalming on Sunday night, avoiding the attention of dozens of media representatives stationed outside.
"We have also told them (North Korea) to come back with a neutral venue, in the event the diplomatic situation is not solved".
The deputy prime minister said the two countries are still negotiating, but did not elaborate.
Kim Jong Nam, who had been living in the Chinese territory of Macau under Beijing's protection, had spoken out publicly against his family's dynastic control of the isolated, nuclear-armed North Korea.
Trump's wiretap claims not supported by documents from Justice Department, source says
Reuters reported earlier this week that an unidentified British security official had denied the allegations about Trump. On Friday, Fox News anchor Shepard Smith said on the air that "Fox News can not confirm Judge Napolitano's commentary.
Kim Jong-nam was not known to be seeking political power, but his position as eldest son of the family that has ruled North Korea since it was founded could have made him appear to be a danger to his half-brother Kim Jong-un.
He explained that as the match was originally part of Matchday 1 calendar of the qualifications, the postponed North Korea-Malaysia tie must be played before the second matchday on June 13.
Yun appreciated Singapore's "faithful implementation" of United Nations Security Council resolutions, stressing the importance of keeping the pressure put in order to reconfigure North Korea's strategic calculus, according to the ministry.
The situation worsened subsequently, when the Malaysian Government also banned North Koreans in Malaysia from leaving the country, after North Korea barred 11 Malaysians from leaving that country.
He was speaking to reporters after launching the new VIP facilities of the Kuala Lumpur International Airport (KLIA) here Wednesday.
The police chief has said he believes the other three are hiding in North Korea's embassy in Kuala Lumpur, Agence France-Presse reported.