World and European champions Spain are three points ahead in Group I and host Georgia in their final qualifier on Tuesday when second-placed France, who look certain to go through to the playoffs, entertain Finland.
The playoff seeds will be determined by FIFA rankings and 25th-placed France face a likely clash with another big footballing nation.
Les Bleus believe the system is flawed because fewer ranking points were available in five-nation Group I while the other sections all contained six teams.
"We're going to contact (FIFA)," French Federation president Noel Le Graet told the radio station RMC. "There is a little injustice between the group of five and the groups of six.
"Our rivals from other groups have been able to score more points ... that's a fact."
Asked if he had discussed the issue with Le Great, coach Didier Deschamps said he was not aware of a potential appeal.
"I don't know if my president will bring the case," he told a news conference at Stade de France.
"I wouldn't go that far in saying there's an injustice but the fact is that we are sanctioned," he added.
"I see it from my position, from an ethical point of view. It's already complicated to be in a group of five and we also lack some points."
Captain Hugo Lloris also found it hard for a team who won the 1998 World Cup and reached the final in 2006 not to be seeded although he recognised it was up to the players to improve the rankings.
"It shows us how much work we have to do. France should be seeded because of their history," he said.
"Our ranking has put us in a difficult position but we have to make do with it. It requires us to work harder, to make more effort."