South Korean President Lee Myung-bak has asked China to deal with North Korean refugees "in accordance with international rules".
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.
A campaign backed by South Korean celebrities to call for the refugees' release has also been started.
China's stand on the North Koreans is not a new policy - for many years it has been sending back those it finds within its borders.
But according to the BBC's Lucy Williamson, the recent change of leadership in North Korea has reportedly led to a crackdown on those trying to escape the country.
Some North Korean groups in South Korea say that harsh penalties of prison camps or death have been promised not just to the refugees themselves, but also to three generations of their families.
It is estimated that more than 20,000 North Koreans have fled to the South since the 1950s, the majority of whom escape via China.