French sports minister Roxana Maracineanu and FFF president Noel Le Graet released a joint statement on Wednesday in which the latter "affirmed his commitment to the sports minister in the fight against all forms of discrimination".
They called for confidence to be placed in referees to stop matches when required and for supporters and clubs "to fight together against all forms of discrimination".
The show of solidarity came after a war of words erupted between the pair on Tuesday, with Le Graet saying that stopping matches for anti-gay chants and banners was "a mistake" in an interview with France Info.
"I would stop a match for racist chants," he added in contrast.
Maracineanu, a former Olympic swimmer, hit back, saying Le Graet had been "wrong" in "differentiating between homophobia and racism".
Since the start of the season, several high-profile matches in France have been halted by officials due to perceived homophobic chants and banners in stadiums.
Among those were Marseille's 2-1 win at Nice last month, which was stopped for 10 minutes. Another game, between Metz and Paris Saint-Germain, was also briefly halted for a banner unfurled by the hosts' supporters asking the league to allow them to aim homophobic chants at PSG.
The interruptions have drawn huge criticism from supporters around the country, but have been widely praised by politicians, led by Maracineanu and equalities minister Marlene Schiappa.
Le Graet received support from France coach Didier Deschamps for his comments, but others in football feel differently, including France striker Antoine Griezmann.
"For me stopping matches, either for homophobic chants or racist chants, is a very good thing," Griezmann, who earlier this year appeared on the cover of the magazine Tetu, a leading gay publication, told RTL.
"If we stop matches, people won't be happy and they will stop doing it," added the Barcelona striker, who has never played club football in the land of his birth.
Meanwhile, the French league on Wednesday called on politicians to "let us get on with the job" in leading the fight against homophobia in stadiums.
"Politicians need to have faith in us and let us get on with the job," said Didier Quillot, the Director General of the Professional Football League (LFP), which runs football in the top two divisions in France.
Quillot was speaking at a press conference in Paris following a meeting between supporters representatives and anti-discrimination groups.
With club football returning in France this weekend after a break for international matches, LFP president Nathalie Boy de la Tour admitted that it was "a crisis situation".
"For a long time we have tolerated certain chants in stadiums, but today society no longer accepts them," she said, while pointing out that only seven matches in total had been interrupted since the start of the season, and for a total of 20 minutes.
"There might be very big differences in terms of how words are perceived...when our supporters express themselves in a certain manner, they don't necessarily pick up on the discriminatory character of the words."
But, amid fears that more matches could be interrupted this weekend in Ligue 1, Quillot said that delegates from the league had been instructed to inform referees only when "discriminatory words" are heard, rather than "insults".
Then it will be up to the referee to decide whether to stop the game.