The union reiterated its call for a mandatory rest period of at least four weeks between the final game of one season and the start of pre-season training for the next.
"Players are coming under too much pressure, caught between the needs of their clubs and their own personal well-being," said the union in a statement.
"While FIFPro understands the financial implications of the UEFA Champions League and UEFA Europa League for clubs, the health of these players is being put at risk because of such a congested match schedule."
The group stage of the World Cup in Russia, which was officially part of last season, finished on June 28 while the final was played on July 15.
The first round of qualifying for this season's Champions League began on July 10, meaning that the two seasons in effect overlapped by a few days.
Iceland's Arnor Traustason played -- and scored -- for Swedish champions Malmo in a 3-0 win away to Kosovar side Drita in a Champions League qualifier on July 10.
Serbia World Cup squad members Nemanja Radonjic and Milan Rodic played for Red Star Belgrade in a Champions League qualifier on July 11 and compatriot Vladimir Stojkovic played for Partizan in the Europa League the following day.
While clubs from smaller leagues are already involved in European qualifiers, big clubs are on lucrative tours abroad.
On Sunday, Manchester United manager Jose Mourinho said his team's World Cup participants should consider cutting their holidays short to help the depleted team in the opening stages of the Premier League season.
Several players from United's first-choice starting line-up, including Frenchman Paul Pogba, Belgian Romelu Lukaku and Englishman Jesse Lingard could miss the opening league fixture against Leicester City in less than two weeks' time.
England defender Phil Jones and forward Marcus Rashford are expected to return early to help prepare for the start of the season.
Mourinho, frustrated after seeing his side lose 4-1 to Liverpool in the U.S. on Saturday, has suggested that others should do the same.