BEIJING—China lodged a rare diplomatic protest with Pyongyang after a North Korean man reportedly killed four Chinese citizens, in the latest sign of strained relations between the two governments.

The protest followed separate reports Monday by South Korea’s Yonhap News Agency and Dong-A Ilbo newspaper that the man, believed to be a runaway soldier, crossed into China in search of food and either shot or beat to death the four people on Dec. 28 in the border city of Helong. The newspaper said Chinese authorities had captured the alleged perpetrator.

China’s foreign ministry didn’t directly confirm the killings but when asked about the reports a spokeswoman said Beijing had “launched representations” with Pyongyang. “China’s public security department will handle this case in accordance with the law,” the spokeswoman, Hua Chunying, said at a daily media briefing. She said she didn’t have additional information.

It isn’t unheard of for North Korea’s poorly fed soldiers to slip over the porous border with China to steal food or other goods, but it is “highly unusual” for Beijing to publicly acknowledge such incidents, according to Andrei Lankov, an associate professor at South Korea’s Kookmin University.

“The Chinese are showing their displeasure,” Mr. Lankov said. Relations between China and its smaller neighbor haven’t been this tense since the early 1990s, when Beijing normalized relations with Seoul, he said. The Koreas have never signed a peace treaty following the 1950-53 Korean War.