FIFPro said that it had "serious concerns" about the situation in the country where important decisions, such as the one to switch the domestic calendar, were being taken without consulting the players.
"The Russian football association (RFS) does not tolerate any involvement of the players," said FIFPro on its website.
"There is not a single representative of the players on the board of the RFS. There is not even any ex-professional player on the board."
The Russian FA was not available to comment.
FIFPro said that, as far as it was concerned, the players were represented by Union of Football Players and Coaches of Russia (PSFT), led by Vladimir Leonchenko.
But the Russian football authorities had instead been pressuring players to join a new organisation known as the All Russian Union of Football Players, it said.
"The RFS and the football league are trying to sideline the players' union and even want to set up their own players' organisation," said FIFPro.
"The league has instructed the clubs in writing to supply the players for this new organisation."
"FIFPro refuses to accept this course of affairs and is involving FIFA and UEFA, amongst others, to help with the situation."
In September, the Russian FA said the March-November calendar would be changed to August-May from 2012/13, despite the notoriously harsh winters in much of the country.
"It is obvious that this system will be accompanied in Russia by an increase of the number of artificial pitches in most of the regions," said FIFPro.
"The percentage of the players opposed to these changes is very high, about 80 percent."
