A meeting of the club's board of directors accepted Starkov's resignation, and named Vladimir Fedotov as acting head coach, the nine-time national champion's press service said.
Spartak's board of directors said Wednesday in a press release that it was satisfied with Starkov's work at the club, but that his resignation had been forced by conflicts at the club at the beginning of the new seasons.
Spartak has made a bad start to the season, and Starkov also drew heavy criticism from captain Dmitry Alenichev, who said earlier this month in an interview with a popular sports newspaper that Starkov's words and actions were irresponsible and he was not qualified enough to bring the club to a European level.
Alenichev was subsequently transfer listed by the club's board of directors.
Starkov, 50, came to Spartak following the 2004 European Championships, where he was in charge of the Latvian national team. Last year, he took Spartak to the second place in the Russian Premier League championship and qualification for the Champions League.
This season has been a different story, as Spartak has played six games for only one victory, one defeat and four draws. It is currently tenth in the championship.