"Supporters shooting at their own players... this is beyond imagination," FIFPro secretary general Theo van Seggelen said in a statement.
"In 2018 Russia is hosting the World Cup. But I cannot imagine many players looking forward to going to this tournament, knowing that their safety is not but guaranteed."
In Friday's incident, a group of fans in camouflage arrived at the club's base in the town of Novogorsk, just north of Moscow, and fired a barrage of paintballs at players and staff.
Reports said fans also scattered leaflets addressed to the club's foreign players such as former Germany striker Kevin Kuranyi, Australia international Luke Wilkshire, Hungary's Balazs Dzsudzsak and Ecuador's Cristian Noboa, warning them to boost their performances or pay the consequences.
"This is another warning that the Russian FA and the national authorities need to step up their efforts in order to protect all professional footballers from hooligans," Van Seggelen added. "I think we might be lucky that none of the players suffered a severe injury, or even worse."
"Unfortunately, this is not the first time that footballers in Russia have been victims of so-called fans behaving violently," he said.
FIFPro has frequently complained about treatment of players in Eastern Europe and has published a so-called black book illustrating some of the worst abuses.