Yusuf Namoglu, chairman of the MHK since 2011, submitted his resignation to the Turkish Football Federation (TFF) and the move will be made official on Wednesday, NTV said.
The TFF and MHK were not immediately available for comment.
Major clubs including Istanbul giants Galatasaray and Fenerbahce say their teams have been targeted by referees during key moments in matches.
Fenerbahce said it would hold a news conference on Thursday to discuss "the repeated, systematic referee mistakes" that have hurt its results. The second-most decorated club in the country, Fenerbahce are currently 14th in the league after 21 matches.
(Reporting by Tuvan Gumrukcu; Editing by Hugh Lawson)