UEFA said its Club Competitions Committee - composed of representatives from top clubs and national associations - expressed its "surprise and concern" at recent FIFA rulings on the release of players.
"This committee is seriously concerned over the confusion and uncertainty created by the recent actions of FIFA in relation to the release of players and the new rules governing international transfers," it said.
UEFA said FIFA had "effectively withdrawn" a recent circular to clubs and national associations sent after the introduction of a new international transfer system in September.
After a meeting of its Players' Status Committee on Wednesday, FIFA said it had confirmed that clubs had to release French players for eight friendly internationals per year. The world champions' game in Melbourne is their eighth of 2001.
Leading European clubs, led by England's Arsenal, had complained that their players would be left exhausted by the long trip in the middle of a hard season. FIFA had earlier recommended that France and Australia select only one player from each club.
FIFA changed its mind over whether clubs would have to release players before the weekend to travel to South America for World Cup qualifiers.
UEFA said: "In particular we would register our grave concern over the handling of the release of players issue whereby provisions contained in the official circular letter on the obligations of clubs and the dates to be applied are now being changed by the latest FIFA decisions.
"We believe major difficulties are being caused by this confusion and would want to see clarification in the rules governing both the release of players and international transfers."
France coach Roger Lemerre called up four Arsenal players on Tuesday, and two from Manchester United and Chelsea, saying he would not bow to attempts to hold his internationals "hostage".
The new transfer system was a compromise deal thrashed out by soccer's governing bodies and the European Union over six months of fractious negotiations during which UEFA president Lennart Johansson and FIFA president Sepp Blatter fell out spectacularly.
The EU's executive, the European Commission, had insisted the former system, where clubs demanded a fee for in-contract players, broke the bloc's employment rules.
Key elements of the deal were that players had to honour their contracts within the first two years of a three year "protected" period or face a four month ban; compensation for clubs training young players; one main transfer window per season; and compensation to be paid if a contract is breached.
European soccer's ruling body UEFA has attacked FIFA in a growing club-versus-country row after the world body backed France's right to call up a full-strength squad for a controversial friendly in Australia on November 11.
