The chairman of the Czech Football Association (FACR), Miroslav Pelta, resigned earlier this week after police charged him with abuse of power, breaching fiduciary duties and favouritism in public tenders. The official denied any wrongdoing.
The Gambrinus brewery, controlled by Asahi Group Holdings, has sponsored Czech football on all levels since 1997. The top league bore its name until 2014.
"The cases around top football and the long-term unwillingness of the FACR leadership to take substantial steps to improve its reputation are damaging us, too," Gambrinus's marketing manager, Marek Dvorak, said on the brewery's website.
"We will continue to support football on lower levels, where we feel there is true joy of the game and fair play," Dvorak said.
The football association has struggled with corruption and match-fixing allegations in the past. Several managers and players have faced sentences for criminal convictions, but never a sitting chairman.
The Czech side, currently third in Group C behind Germany and Northern Ireland, plays Norway on Saturday in their next qualifier for the 2018 World Cup. The Czechs last played at the world's top tournament in 2006.
(Reporting by Robert Muller, editing by Larry King)