Jean-Pierre Rafarrin said on Sunday he was opposed to an "ostentatious display of religious conviction" in the nation’s lycees.
His supporters say that preserving France’s secular tradition is essential to ensure the equality of all in society.
They say outward displays of religious affiliation threaten the very underpinnings of the French state.
But Muslim groups complain their religion and culture are being attacked by secular extremists.
They say the onslaught is more likely to alienate Muslims from French society rather than endear them to it.
There are approximately five million Muslims in France today, nearly one tenth of the country's population.
Muslims started arriving in significant numbers in the 1960s, when the government granted asylum to hundreds of thousands of Algerians who fought for France in Algeria's war of independence.
At the same time, it opened its doors to immigrant manpower to meet the needs of its burgeoning economy.
And despite "zero immigration" laws enacted in the 1970s, France’s Muslim population continues to rise, thanks largely to high birth rates.
Facing this situation, France's policy has been to integrate the Muslim community into society in an attempt to make it more "French".
Yet, as poll after poll shows, in the French mind Islam is still linked with “fundamentalism”, oppression of women and “terrorism”.
And to say the least, the Muslim community lives uncomfortably in France.
They regularly complain of racism, religious discrimination, social exclusion and under-representation.
Moreover, some accuse the French state of trying to control, even water down, their religion.
A few months ago, Interior Minister Nicolas Sarkozy said Paris should open a seminary to train imams to fight the spread of "Islamic fundamentalism".
He added the training institute should produce imams who speak French and who are imbued with "our culture".
And in April Jean-Pierre Raffarin told a new Muslim umbrella group he expected it to be the "enlightened voice of Islam" and to combat threats to the country's social cohesion.
Both statements were seen by many as a direct attempt to sideline practising Muslims from national life.
But it is the current debate over headscarves in schools which is really exposing the uneasy relationship Muslims have with France and with government ministers facing allegations of racism.
Raffarin says France's secular
tradition ensures equality
The arguments were reignited earlier this year when Sarkozy insisted Muslim women should remove their headscarves for identity card photographs.
A Muslim group leader, Abd Allah Ben Mansour, responded by comparing government rules on ID card photographs to Nazi laws against Jews.
There have also been several protests against Muslim pupils wearing headscarves in classrooms up and down the country.
Teachers in the small town of Flers even went on strike when a 12-year-old pupil refused to remove her veil.
In the face of this perceived discrimination, there is no doubt many devout Muslims feel considerable anger.
But France's Muslim organisations prefer quiet diplomacy to open confrontataion with the French state.
Most say they respect France’s secular tradition, but see no contradiction between it and Islam.
Lhaj Thami Breze, president of the Union of French Islamic Organisations, told Aljazeera: “We respect secularism and sincerely believe it respects Islam and all religions.
"Our argument is only with secular extremists who want to ban the veil. People often talk of religious extremists but there are secular extremists as well."
But other French Muslims' groups, such as the Muslim Co-ordinating Committee, have gone as far as to defend Sarkozy, saying it was "shocked by the disgraceful behaviour of those who dared to defy the republic".
Findings by a national commission on France's secular principles are due to be made public shortly.
There is much speculation about whether it will recommend that new legislation is enacted to ban the Islamic veil in French schools.
But even if it does not, this will offer scantt consolation to France's Muslim community.
For as long as influential secular extremists are around to rigidly intepret France's constitution, life for many Muslims will continue to be uncomfortable.