World governing body president Sepp Blatter said on Tuesday FIFA could suspend the French Football Federation (FFF) if France's politicians kept meddling in football.
That means the country could be banned from international tournaments and French clubs could not take part in European competitions.
"There was never any question of the French government interfering in the affairs of the French Football Federation," French government spokesman Luc Chatel told reporters on Wednesday.
FFF president Jean-Pierre Escalettes resigned on Monday in the wake of France's disastrous showing in South Africa, saying the decision was his own, but sports minister Roselyne Bachelot had said last week his resignation was "unavoidable".
"She (Bachelot) indeed indicated that she personally believed his resignation was unavoidable but she did not ask for his resignation," Chatel said.
France's woeful campaign sparked a national debate in France with senior politicians getting involved. Bachelot appeared before a parliamentary commission on Tuesday, and on Wednesday Escalettes and outgoing coach Raymond Domenech did the same.
"It is normal for members of parliament to try to find out exactly what happened because it is a topic that preoccupies French people," Chatel said.
France left the World Cup at the group stage after a campaign rocked by the players' decision to boycott a training session in support of striker Nicolas Anelka, who was sent home for insulting Domenech.
While Nigerian President Goodluck Jonathan suspended his national team from international competition for two years following their poor World Cup performance, France took a different route with high-level meetings over the fiasco.
HELPLESS ESCALETTES
Escalettes told the parliamentary commission on Wednesday he had felt helpless against the player revolt that led to him handing in his resignation.
The FFF official said he could do nothing to stop the players boycotting a training session in support of expelled striker Anelka.
The 75-year-old Escalettes told the commission about the incident at Knysna in South Africa's Western Cape, and how he had tried to convince the players sitting on the team coach that refusing to train was not a good idea.
The players, who eventually left the World Cup in disgrace with just one point and one goal from three group matches, would not listen and continued the boycott to protest against the FFF decision to kick out Anelka after he had insulted Domenech.
Escalettes and Domenech told the commission they had tried their best to reason with the rebellious players.
"He (Escalettes) told us that in the coach they (Escalettes and Domenech) had used every conceivable argument in vain," commission member Lionel Tardy told reporters after Wednesday's hearing, that took place behind closed doors.
"Escalettes told us they faced a wall (of opposition), something he had never experienced in over 50 years in football, and they could not make it fall," he added. "For him, something was bro
