Ri Jong-Chol is among eight North Koreans suspected of involvement in the dramatic killing of Kim Jong-Nam, the half-brother of the reclusive nation's leader, who was poisoned with a banned nerve agent at Kuala Lumpur International Airport.
Malaysia's attorney general had announced there was insufficient evidence to charge 47-year-old Ri.
The North Korean was deported Friday night, a government official, who asked not to be named, confirmed to AFP.
"He will be escorted by two North Korean officials to Beijing and from Beijing to Pyongyang," deputy prime minister Ahmad Zahid Hamidi told reporters earlier. "We have also blacklisted him and he cannot enter this country again."
"The police probe showed he was not working as stated in his documents but was involved in illicit activities detrimental to our security."
Earlier, as he was led out of a police station outside the capital under tight security and handed over to immigration authorities, police chief Khalid Abu Bakar said he regretted the release.
"We believe that Ri Jong Chol played a part in Kim Chol's murder but unfortunately we lack evidence to charge him," he told AFP, using the name given in the passport carried by Kim Jong-Nam.
"We are frustrated because of a lack of evidence," he said via text message from Saudi Arabia where he is on a religious pilgrimage.
However, he denied political or diplomatic pressure had been a factor in the release, saying it was purely an investigative issue.
Ri's release came two days after two women -- one Vietnamese and one Indonesian -- were charged with murdering Kim.
Seven other North Koreans are wanted in connection with the killing.
