Germany's Borussia Dortmund said they were against midfielder Shinji Kagawa travelling to Argentina for the July 1-24 Copa America, at which Japan are a guest team.
Schalke 04 full-back Atsuto Uchida and VfB Stuttgart striker Shinji Okazaki have also been told they will not be able to go to South America.
Japan's domestic J-League clubs are also unable to release players with the season postponed following last month's deadly earthquake and tsunami.
"The agreement we reached with the Japan Football Association (JFA) is that the J-League would release seven or eight young players," the J-League's Hisao Shuto told Reuters on Monday.
"The rest of the 22 players would come from Europe. The understanding was the South American federation (CONMEBOL) was to negotiate with FIFA for the release of the other 14 or 15.
"We have a league to play and those were the conditions agreed. We can't change the schedule of the J-League again."
Japan last week reversed its decision to pull out of the Copa America after the deadly March 11 earthquake and tsunami which devastated much of the country's north-eastern coast.
But despite assurances from CONMEBOL to help with the release of players at European clubs, FIFA have refused to bend the rules to ease Japan's problems.
"We have to play our league games," said Urawa Reds media officer Daisuke Maruyama. "That's our top priority."
Soccer, as all sports across Japan, was left in chaos following last month's disaster which left 28,000 people dead or missing and triggered a nuclear crisis at a power plant north of Tokyo.
Stadiums suffered damage while the J-League have been forced to cram a month's worth of games into three weeks in the stifling July heat to make up the backlog of lost matches.
Borussia Dortmund became the latest European club to frown on Japan's trip to the Copa America on Sunday, saying their injured midfielder Shinji Kagawa needs a proper training camp this summer ahead of what will be his second Bundesliga season.
"Shinji is coming off a serious injury, and it's necessary for him to prepare with the team before the new season," Dortmund's sports director Michael Zorc said.
"That would be the best decision in his interests. We have a very good relationship with the Japan Football Association. We talked to them when they came over to Germany for January, and we will certainly speak with them again this time."
Kagawa, who has become a key member of a new-look Japan side under Italian coach Alberto Zaccheroni, has been sidelined since breaking a metatarsal at the Asian Cup in January.
