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However, Fifa have said that if Manchester City field Anelka in their match against Middlesbrough on Saturday, the club could have match points deducted and face a heavy fine. City deny this is the case.
"Article 40 of our rules are very clear on this," fifa told BBC Sport Online.
"If he has refused to play for France, Anelka cannot play for his club during the time he should be on international duty.
"He would also be unable to play for the club for five days after the match, which means he cannot play for Manchester City until next Tuesday."
Fifa said the only grounds on which Anelka could escape a ban is if he had retired from international football for good.
"If the player has made it expressly clear to his federation that he is no longer available for national team selection, then there would be no grounds on which to invite him.
"But this cannot apply to situations where the player has only declined to play certain games," Fifa said.
However, City believe that Anelka is exempt from the rule because he was called up as a last-minute replacement after Govou was injured.
City quoted Article 38, Section Two of the FIFA rulebook stating: "A national association wishing to summon one of its players who is playing abroad must notify in writing at least 15 days before the date of the match. The player's club should also be informed."