Choi, chairman of the government-run Korea Communications Commission, stepped down after prosecutors arrested his aide, Jeong Yong-wook, on charges Jeong illicitly received money from Kim Hak-in, the operator of a local broadcasting school, the Yonhap News Agency reported.
Kim was arrested on embezzlement and tax evasion charges last week, Yonhap said.
The departure of Choi, a key supporter in President Lee Myung-bak's administration, came during negotiations about sweeping changes in broadcasting law, the news agency said.
A 2009 law eased regulations and allowed cross-ownership of newspapers and broadcasting stations, leading to the launch last month of four new cable television stations and a news channel, significantly altering South Korea's media structure.
Notable deaths of 2014 [PHOTOS]