Checks by the French Interior Ministry on the number of Muslim children who skipped school last month to celebrate Eid Al Fitr drew criticism from trade unions and anti-racism groups on Monday.
The festival concludes Ramadan and is observed as a holiday in Muslim-majority countries.
This year, Eid Al Fitr fell on Friday, April 21, for most believers.
"An evaluation of the level of absenteeism recorded on the occasion of Eid Al Fitr" was ordered by France's Interior Ministry on Sunday.
The ministry "regularly studies the impact of some religious festivals on the workings of public services, and notably in the educational sector", junior minister Sonia Backes said in a statement.
In the city of Toulouse, police asked the heads of local schools to report the number of children absent on April 21, leading to accusations that authorities were creating a registry – which was denied by Ms Backes.
The country's biggest teachers' union, the FSU, said in a statement addressed to Interior Minister Gerald Darmanin on Monday that it "harshly denounces this operation".
"Attempting to create statistics by security forces on religious beliefs and their observance or not, above all in a school environment, goes against the basic principles of secularism and fundamental rights," the FSU said.
Eid Al Fitr preparations around the world - in pictures
The smaller CGT Education union called it a "scandalous and dangerous stigmatisation".
Using police to carry out the checks was "particularly shocking because it associates the observance of the Islamic religion to an issue of security", the anti-racism group SOS Racisme said.
France has a strict form of secularism that seeks to separate the state and its various branches from religion and religious bodies, while guaranteeing the freedom to worship to all.
Collecting information about ethnicity or religious beliefs is also generally prohibited in France under the country's anti-discrimination laws.
Owing to the country's Catholic heritage, major Christian festivals such as Christmas or Easter are observed as public holidays in France, and schools are closed.
