KUALA LUMPUR, Malaysia—Malaysia’s government said Saturday it would expel North Korea’s ambassador to the country, a day after police issued an arrest warrant for a North Korean airline employee in connection with the death of the estranged half brother of dictator Kim Jong Un.

Foreign Minister Anifah Aman said the ambassador, Kang Chol, has been given 48 hours to leave the country, after he failed to attend a requested meeting with officials Saturday.

Relations between the two countries have deteriorated since Malaysia named several North Korean suspects in the killing of Mr. Kim’s half brother, Kim Jong Nam, at Kuala Lumpur International Airport on Feb. 13. Malaysian authorities have said they believe Kim Jong Nam’s death was planned by a hit squad of North Korean nationals.

Mr. Anifah’s statement suggests officials were angered by the North Korean ambassador’s criticism of Malaysia’s investigation. Other North Korean officials have accused the Southeast Asian country of conspiring with South Korea and the U.S. to make it appear as if agents from Pyongyang had killed Kim Jong Nam.