'Transplants should not be a privilege for the rich,' Huang said, apparently responding to public criticism of the current system.
Huang admitted that some hospitals 'ignore legal procedures' to make a profit from the organs of executed prisoners.
For example, organ donors were sometimes persuaded to sign documents claiming they were relatives of or 'emotionally connected' to wealthy transplant recipients, the newspaper said.
It said the new system was also designed to prevent 'transplant tourism', where wealthy foreign patients paid for transplants in Chinese hospitals.
China banned the commercial trade of human organs in 2006 and required written consent from organ donors.
It caries out an estimated 8,000 executions a year, more than the rest of the world combined.