Jiri Dvorak, Fifa's chief medical officer at the World Cup, confirmed there had been an increase in the number of non-contact injuries, such as strained muscles, when no tackles are involved.
Dvorak said: "Professional footballers are definitely playing too many games.
"If there is not sufficient time to recover or they don't recover completely, there can be an accumulation of injuires that can lead to one major injury.
"Some players are playing between 80-90 games a season and that is too much."
Germany's former World Cup-winning captain and coach Franz Beckenbauer laid the surprise exit of major teams like France firmly at the door of fatigue.
In contrast, co-hosts South Korea have benefitted from the majority of their squad not having been pushed through a punishing European season.
That has shown in the Korean's high tempo game which has made them the surprise packet of the tournament.
Dvorak is keen to launch a scientific investigaiton into injuries and burn-out among top players following complaints that the World Cup has been spoiled by the sight of exhausted players on their last legs.
Figures show that while the number of injuries per game are similar to previous World Cups, there has been a dramatic increase in non-contact injuries, from 14% in past tournaments, to 26% of all injuries at this tournament.
Fifa's comments come in the wake of calls from England coach Sven-Goran Eriksson, and Arsenal manager Arsene Wenger to cut the size of the English Premiership.
Dvorak confirmed there was no sign that players were taking increased amounts of anti-inflammatory drugs and painkillers in order to get fit for games.
So far, the World Cup has produced no positive tests for banned substances, such as stamina-boosting erythropoietin (EPO) which was the drug at the centre of scandals at February's Salt Lake City Olympic games.