"Supporters, clubs and players are all losing out due to a measure which overshoots its aim," FIFPro said in a statement on its website. "The remedy is currently much worse than the disease."
Under the current ruling, a player who takes part in the qualifying competition but is then transferred cannot appear for his new club in the group stage. The same applies to the Europa League.
FIFPro said the rule, introduced because it was feared that players appearing for two different clubs in the same season would discredit the competitions, had been overtaken by events.
"The summer transfer period runs from July 1 to August 31, traditionally a period of preparation and practice matches, but that time is long gone," it said, adding that this season the Champions League preliminary round began on June 29, before the World Cup had finished.
"This has led to an artificial and undesirable situation on the transfer market."
FIFPro said players who had hopes of a move were declining to play in the qualifiers even though a place in the lucrative group stage was at stake.
"A measure which was initially introduced by FIFA in order to combat the distortion of competition is now actually encouraging it," it said.
"More than ever, this season has seen the situation occur in which a player has refused to play for his employer in a European competition to avoid jeopardising his chances of a possible transfer, or a club itself has refused to field a player because it still hoped to sell him," said FIFPro.
FIFPro said Argentina's Javier Mascherano, England's James Milner and Ukrainian Artem Milewski were among those who did not want to play for their clubs in Champions or Europa League qualifiers.
"Dynamo Kiev left Artem Milewski out of the team for the first Champions League qualifying round match against Ajax Amsterdam in order not to jeopardise a possible move to Chelsea or Liverpool," FIFPro said.
"That match ended in a disappointing draw, followed a week later by elimination as a result of which Milewski - for whom no club eventually came in - has to make do with the less prestigious Europa League."
