The country included the abaya in an expanded list of banned religious items that children cannot wear at state schools and 67 pupils were sent home on Monday – the first day of term and the first day of the extension.
On Tuesday, President Emmanuel Macron explained his support for the ban and Education Minister Gabriel Attal said they may have to bring back school uniforms.
Mr Attal said he would provide a timetable in autumn for carrying out a trial run of uniforms with any schools that agree to participate.
“I don't think that the school uniform is a miracle solution that solves all problems related to harassment, social inequalities or secularism,” he said. “We must go through experiments, try things out” to promote debate, he said.
Uniforms have not been obligatory in French schools since 1968 but regularly return to the political agenda, often pushed by conservative and far-right politicians.
Mr Macron defended a government ban on the long-flowing dresses known as abayas in schools, saying it was not an attempt to single out Muslims.
In an interview with a YouTuber popular with young people, he said the decision was made because teachers were worried about religious expressions at schools, and for kids to focus on learning rather than their religious identity.
“School must remain neutral: I don’t know what your religion is, and you don’t know mine,” Mr Macron told the Hugo Decrypte channel.
“I’m not stigmatising anyone,” he added. Families “or young girls who wanted to wear the abaya must understand why we’re doing this”.
Almost 300 girls wore an abaya to school on Monday. Of those, 67 refused to change into alternative clothing and were sent home, Mt Attal said.
France has enforced a ban on religious symbols in state schools since 2004 to uphold its idea of secularism known as “laicite”.
For some, wearing a uniform means equality and erasing differences in social status and wealth. For others, it is a debate that is not needed and is distracting from more serious issues such as discipline and harassment.
An association representing Muslims has filed a motion with the State Council, France's highest court for complaints against state authorities, for an injunction against the ban on the abaya and the qamis, its equivalent dress for men.
The Action for the Rights of Muslims motion is to be examined on Tuesday.