The protest organized online by a socially conservative group urged parents to keep their children home Monday to protest a French Education Ministry pilot program in 500 schools where children ages 6 to 11 are taught about gender equality.
Critics contend the program tells children they can choose their own sexual identity and gender, the Daily Telegraph reported Tuesday.
"The national education system is going to teach your children that they are not born a girl or a boy, as God intended, but choose to become one," Equality and Reconciliation said in its message to parents.
Education officials say the group is wrong and deny children are being taught so-called gender theory.
Education Minister Vincent Peillon said criticism is overblown and those who oppose equal protection for gays and lesbians are mischaracterizing the program's intent.
"Don't worry, this is about education on equality between girls and boys, respect between girls and boys, that's all," he said, adding the criticism schools are "teaching little boys how to become little girls" is "totally false."
The protest has been most widely adopted in immigrant and Muslim communities. Portions of the country home to large numbers of Muslims saw school absenteeism as high as 40 percent Monday.