The girl was stopped from going to class earlier this month by the head teacher who reportedly felt the long skirt -- popular among some Muslim women who cover their whole body -- "conspicuously" showed religious affiliation, which is banned in schools by France's strict secularity laws.
"The girl was not excluded, she was asked to come back with a neutral outfit and it seems her father did not want the student to come back to school," local education official Patrice Dutot told AFP on Tuesday.
He added that the student always removed her veil before entering school premises in the northeastern town of Charleville-Mezieres, as is specifically stipulated by law.
According to the 2004 law that governs secularity in schools, veils, the Jewish kippa or large Christian crosses are all banned in educational establishments, but "discreet religious signs" are allowed.
The student, whom local daily L'Ardennais identified as Sarah, told the newspaper her skirt was "nothing special, it's very simple, there's nothing conspicuous. There is no religious sign whatsoever."
Her story was trending on Twitter in France Tuesday with the hashtag #JePorteMaJupeCommeJeVeux, translated into English as "I wear my skirt as I please."
"If it's worn by a 'white' person, it's hippy chic, if it's a Muslim, it becomes conspicuous," one user tweeted.
But the regional education office hinted in a statement that wearing the skirt could have been part of a concerted "provocation."
"When it comes to concerted protest actions by students, which follow other more visible incidents linked for instance to wearing the veil, the secular framework for education must be firmly reminded and guaranteed," it said.
According to the CCIF Islamophobia watchdog, some 130 students were rejected from class last year for outfits deemed too openly religious.
According to CCIF those incidents included one in the southern city of Montpellier, when several girls were excluded from classes for wearing skirts deemed too long.
"Wearing a long skirt is nothing ostentatious.This is more due to mass hysteria," said Abdallah Zekri, president of the National Observatory against Islamophobia.