Several police officers, including the investigations officer of Jong-nam's murder, had spent about three hours at the North Korean embassy this morning - purportedly to brief embassy officials before they released the body.
The body was carried out of the mortuary in a multi-purpose vehicle at around 1.30pm, the paper quoted a source as saying on its website.
A journalist waits in front of the North Korean embassy in Kuala Lumpur on Wednesday.
Malaysia's The Sun Daily reported the release of Jong Nam's body by the Kuala Lumpur Hospital to be sent to his family by Monday, some 41 days after he was poisoned with the banned VX nerve agent at Kuala Lumpur International Airport 2 on Feb 13.
Apart from Uk-il, the police are also looking for other suspects, including the embassy's second secretary, Kwang Hyon-song, 44, who is still "hiding" at the embassy building, as well as Ri Ji-u, 30, also known as "James", still believed to be in the country.
An official who spoke to online newspaper Malay Mail said that after the change in policy, no North Koreans had entered the country.
In 2014, the International Society for Human Rights, (ISHR), stated that North Korea's crimes are "without parallel" in the contemporary world, documenting examples of widespread torture recorded in North Korea, with orders for brutality often coming from the most senior members of society.
Then Pyongyang barred Malaysians from leaving the country, prompting Kuala Lumpur to expel North Koreans from its soil.
Malaysian authorities maintain that they identified Jong Nam's body based on a DNA sample obtained from one of his children.
Malaysia has arrested three people in connection with the murder.
The South Korean government has welcomed the UN Human Rights Council's adoption on Friday of a resolution condemning the human rights situation in North Korea.
There were rumors that both sides have reached a decision on the remains of Mr Kim Jong-nam paving the way for the 45-year-old's body to be given to Pyongyang.