China is reportedly in the process of repatriating up to 30 North Koreans who were recently arrested.
They could face severe punishment, even death, in the North for leaving, activists say.
China has said that the North Koreans are “illegal economic migrants” who must be returned home.
“When it comes to the North Korean defectors, it is right for the Chinese government to handle them in line with international rules as long as they are not criminals,” Mr Lee said.
His comment comes shortly after South Korea said it would raise the issue with the UN next week.
The North Koreans awaiting deportation were reportedly detained by Chinese authorities in separate incidents.
The issue is gaining attention in South Korea and there have been several protests by human rights groups. An opposition lawmaker has also begun a hunger strike outside the Chinese embassy in Seoul.