"We hate to do this but it is our job to protect the players," FIFPro secretary general Theo van Seggelen said in a statement.
"Players haven't been paid for months and encounter serious financial problems. Clubs are on the verge of going bankrupt.
"On top of that, I received the shocking news that one of the clubs totally disrespects players' rights and even allows hooligans to threaten their players."
SPFN president Mirko Poledica said there were currently 115 cases at the country's dispute resolution chamber.
"The current situation is alarming," he said. "There are only approximately 500 professional footballers in Serbia. We would not be surprised if some of the clubs file for bankruptcy in the near future.
"Therefore we must send a message to all countries and recommend all foreign footballers not to come to Serbia, because there are no guarantees that they will be paid."
FIFPro said that players at first division club Radnicki Kragujevac were threatened by supporters, who were allowed into the changing room, when they went on strike in protest at not being paid for three months.
"One of the more experienced players, Vuk Sotirovic, was hit in the face when he tried to reason with the supporters and protect his younger team mates. Other players prevented a fight from breaking out," FIFPro said.
FIFPro said the Serbian football association (FSS) and League condemned the incident in a letter but the former did not start any disciplinary procedure against the club, which Poledica described as "very disappointing".
At the team's next home game, fans displayed banners with insults and threats directed against the players, and seven players left the club in the following few days, FIFPro added.
The FSS and Radnicki Kragujevac could not immediately be reached for comment.
Serbian football reached a new low in June when last season's champions Red Star Belgrade were barred from the Champions League by UEFA because of unpaid bills.
(This version of the story was refiled to correct play to pay, fix typo in second para)
(Writing by Brian Homewood in Marrakech; Editing by John O'Brien)
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