Benzema was left out of the line-up because he has been named in a criminal investigation into a blackmail case targetting another French national team footballer, Mathieu Valbuena, accrding to French squad manager Didier Deschamps.
But the Algerian-origin striker for Spanish team Real Madrid accused Deschamps of being influenced by a "racist party", a veiled reference to the far-right National Front.
French Minister for Cities, Youth and Sport Patrick Kanner slammed Benzema's claim of racism in Deschamps' decision-making.
"Sport, especially football, is one of best things for integrating communities," he told the media. "What was said or insinuated about Didier Deschamps is completely unacceptable. I defend the manager who made choices based on sports criteria."
Benzema's disappointment was understandable, he said. "But what he said is by no means acceptable, given Mr Deschamps' character and his professional ways."
Socialist MP Benoît Hamon also backed Deschamps, declaring that the French team manager is not racist, while agreeing with Benzema's view that racism is on the rise in France.
The 28 year-old has been capped 81 times in his career and has scored 27 goals in international matches.