Following the release of a Bill promoting secularism in schools last week, Lhaj Thami Breze said girls will face a choice between their education and their conscience.
Mr Breze, president of the influential Union of Islamic Organisations of France, said some Muslim girls are likely to transfer to private schools, including Catholic establishments. "I know that our Catholic brothers are very tolerant," he was quoted as saying in the daily free newspaper Metro.
Education minister Luc Ferry met with Muslim leaders last week to address their concerns.
In December, President Jacques Chirac asked parliament to ban headscarves.
However unlike Germany (see left), the proposed laws also ban other conspicuous religious symbols, such as Jewish skullcaps and large crosses, in public schools to protect secularism in a changing France. The legislation goes before parliament next month.
"The principle of secularism, which expresses values of respect, dialogue and tolerance, is at the heart of France's republican identity," says the Bill, presented as an amendment to the education code.
In state primary and secondary schools "signs and clothing which conspicuously demonstrate the religious (convictions) of students are forbidden", it says.
The Bill has broad support in France, but many of the country's five million Muslims say it will trample on their freedoms. At a demonstration in December, protesters sang the Marseillaise, waved the flag, and shouted "Beloved France, where is my liberty?"
The move has also drawn criticism and protests from numerous Muslim countries and from US State Department officials.
John Hanford, US ambassador at large for International Religious Freedom, said the Bush administration believes that "all persons should be able to practise their religion and their beliefs peacefully without government interference, as long as they are doing so without provocation and intimidation of others in society."
There were protests by children outside the French embassy in Lebanon last week.
Top Muslim Shiite cleric, Grand Ayatollah Mohammed Hussein Fadlallah, said President Chirac's proposal "confiscates" a woman's freedoms and attacks human rights.
In an open letter to President Chirac he said that wearing the headscarf is a "religious duty" for Muslim women.
But Mohammed Sayyed Tantawi, Grand Sheik of Al-Azhar in Cairo, the world's most prestigious Sunni theological institute, said that "if a Muslim woman lives in a country where laws do not permit (the scarf), then she has to comply with those laws."