"The contract of Yuri Krasnozhan is terminated with immediate effect because of negligence in his job," Lokomotiv said in a statement on their website without giving further details.
Krasnozhan was sacked following an executive board meeting late on Monday and the news came as a surprise with Lokomotiv in the top five after a slow start to the season.
"I was shocked by the news, to be honest," Alu Alkhanov, chairman of the Russian FA's ethics committee, told local media.
"But the club didn't break any laws by firing Krasnozhan. It's an internal matter for the club."
Former Lokomotiv midfielder Vladimir Maminov was on Tuesday named caretaker coach for a second time following a brief spell in the job in 2009.
The sacking followed Lokomotiv's surprise 2-1 home defeat by Anzhi Makhachkala last week, their first loss since early April.
"I don't want to say anything at this point. I have to think it over before making any comments," Krasnozhan, who celebrated his 48th birthday on Tuesday, told local media.
He was hired by the Moscow club in December after guiding unfashionable Spartak Nalchik to sixth place last year.
Fifth-placed Lokomotiv have 18 points from 11 games, with the top four all on 19 points. Leaders CSKA Moscow have played one game fewer than their title rivals.
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