FIFPro fully backed a study conducted by Dutch coach Raymond Verheijen which said that two days were insufficient and significantly affected a team's chances of winning.
After studying the results of 27,000 professional matches, Verheijen said he had concluded that rest period of three days “proved sufficient and did not give rise to any noticeable change in the chances during the second match.
FIFPro's technical director Thys Tummers said the devaluation of the Europa League could be a “direct consequence of the two-day rest periods
"Clubs in the Europa League that want to gain a place in the highly lucrative Champions League increasingly favour the (domestic) competition in which they can gain qualification for the Champions League and rest their best players for the Europa League fixtures," he said.
"This has been the consistent policy of Tottenham Hotspur throughout this season. The team was eliminated in the group stage.
"Twente Enschede, even though they had a lead of 1-0, fielded a weakened team for their return match at Schalke 04 and were eliminated.
"This undesirable effect could be avoided in the future by giving players and teams three days' rest between two matches."
Tummers said there were other reasons for following the recommendations.
"First, there is the question of fair play. By allowing one club only two rest days, you give the teams an unequal chance of a good result.
"In addition, we must take care that our players are not overused. First, because of the health of the players, but second, because the public want to see the players perform at their best.
"That doesn't happen after just two rest days. It is plausible that the number of injuries is higher after only two rest days; a follow-up study is currently being held into this."
FIFPro said that Portugal was the only country where players were guaranteed three days' rest with teams involved in the Europa competition allowed to play their next league matches on the following Monday.
In his study, published last week, Verheijen, who has worked on the coaching staff of the Netherlands, Russia, South Korea and Wales national sides, analysed results of English Premier League teams during the group stage.
He said: "The eight worst results all came after two-day gaps -- Manchester City's away defeats to both Bayern Munich and Napoli, Manchester United's home draws against Basel and Benfica, Chelsea's away draw with Genk and defeat to Leverkusen and Arsenal's draws with Dortmund and Marseille.
"The fact that Spurs are still well placed to qualify for the Champions League is absolutely down to Harry Redknapp's refusal to play his first team in the Europa League last year," he added.
Verheijen also calculated that Europa League winners Atletico Madrid's campaign in the competition could have cost them six points in La Liga.