The 75-year-old Swiss has been widely criticised after saying in two television interviews on Wednesday that there was no racism in football and that players involved in racist confrontations on the pitch should settle their differences with a handshake at the end of the match.
FIFPro said it had worked well with football's governing body to battle racism until the 2010 World Cup in South Africa, but that since then FIFA had gone quiet on the issue.
"FIFPro has been fighting racism for many years now and tries to convince the football world of the fact that all men are equal, that racism does not belong to football nor to society," the Netherlands-based organisation said in a statement.
"In the past FIFPro successfully worked together with FIFA in the fight against racism, but since the 2010 World Cup in South Africa, FIFA has hardly made itself heard on this fight, which is rather sad.
"The fact is that it is not sufficient to have both captains read out a declaration before the beginning of the match, under the watching eye of the whole world, as was done during the quarter-finals of the 2010 World Cup.
"This battle is not so easy to win. This battle has to be fought continuously, and not only during the World Cup."
FIFPro agreed with Blatter that players did not always behave well on the pitch but said there was a limit.
"The statements of Mr. Blatter are, to put it mildly, rather clumsy," said FIFPro.
"There is a bottom line which should not be crossed. There are things that you cannot just solve by shaking hands after the end of the match, as Mr. Blatter suggests.
"Unfortunately racism remains a huge problem in football, both on the pitch and in the stadiums. FIFPro is well aware of this and so is Mr. Blatter."
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