France coach Raymond Domenech has alleged that his players were subjected to racist taunts by Spanish fans before Tuesday's second-round match.
Domenech and Henry savour France's win over Spain
He said: "When I arrived with the bus there were fans making monkey chants."
The claim seems certain to reignite the racism row that has plagued Spanish football in recent years.
In 2005 Spain coach Luis Aragones was fined for making racist remarks about France's Thierry Henry and players have suffered racist abuse in La Liga games.
Aragones' comments about Henry were the most high-profile and Henry was clearly delighted that France were able to beat the Spaniards in Hanover on Tuesday.
The Arsenal striker said: "A lot of people were speculating about Aragones and I don't want to talk about it because there is no point.
"But the best answer was the win."
The first responsibilities lie with the national associations
In November 2004 Fifa fined the Spanish Football Federation (RFEF) £44,750 after several England players were racially abused during a friendly match in Madrid.
And last year Real Zaragoza and Racing Santander fans racially abused Barcelona forward Samuel Eto'o during league matches and were subsequently fined by the RFEF.
Domenech's claims come on the day that Fifa warned they will suspend national associations who fail to impose tough new rules on racism that come into force in July.
Fifa president Sepp Blatter said the regulations - including docking points from clubs and countries whose fans are guilty of racism offences - were mandatory.
Blatter stated: "The first responsibilities lie with the national associations and if they are not doing what is expected of them then Fifa's executive committee must intervene.
"The power and the responsibility lies with Fifa and the suspension of a federation is the ultimate sanction available to the disciplinary committee."
He added: "This is a fight against a devil that still exists, unfortunately, in our sport."