The runaway soldier shot four Chinese citizens after a robbery attempt in late December in Helong, a city near the Tumen River that divides the two countries.
China's foreign ministry spokesperson said North Korea voiced regret over the incident after China lodged a formal diplomatic complaint against them on Monday.
"The DPRK side expressed its regret that such incident happened, and conveyed its sympathy to the family of the victims," said Hong Lei, spokesperson for China's Ministry of Foriegn Affairs in a press conference.
The defector was shot by the Chinese police in a manhunt operation, and has died from injuries suffered during his capture according to the ministry.
He added that the incident is being handled as an individual criminal case.
There have been previous reports of runaway North Korean soldiers and citizens attempting robbery in search of food.
A restaurant owner who lives in Dandong, another city bordering North Korea, recalled a harrowing incident in early 2013.
"One night, I heard a dog barking outside, so I got up to check what was going on. In the dim lighting, I saw a man dressed like a North Korean soldier stealing things from my restaurant," the unnamed owner was quoted in The Global Times
"I yelled at him and he held up his gun as if he was ready to shoot. I was terrified and ran back to my room. He stole some meat and fled by speedboat."
In most cases, intruding soldiers were after food, and do not have the intention to harm people, making it rare that such violent cases would occur, reported the Chinese state-run newspaper.
Thousands of North Koreans have tried to flee the country in hopes to escape the totalitarian regime. However, China has a uniform policy for sending defectors back to North Korea, ruling them as "illegal economic migrants."