Health department director general Thami Mseleku has resigned three months before his five-year contract runs out, spokesman Fidel Radebe said on Sunday.

"This is by mutual agreement between him and minister Aaron Motsoaledi," Radebe told Sapa.

He confirmed Mseleku would be leaving the department at the end of the month.

Mseleku's tenure has not been without controversy. He has been criticised for poor administration and for reportedly seeking to ban provincial health officials from speaking on HIV/Aids matters.

City Press newspaper quoted Mark Heywood from the Aids Law Project welcoming his imminent departure as a sign Motsoaledi "is serious about improving the health care system".