The president of the Marseille Israelite Consistory, Zvi Ammar, said that it was an "exceptional decision".
"Life is more sacred than anything else. We are now forced to hide a little bit," he told the AFP, adding that the move made him "sick to the stomach".
But shortly after the country's chief rabbi Haim Korsia, told Jews in France to ignore the call from Ammar and continue wearing the traditional headwear, also called the Kippah.
"We should not give an inch, we should continue wearing the kippah," Korsia said.
The warning from Ammar comes just one day after a teacher in his thirties was attacked by a teen wielding a machete.
The teacher escaped with only minor injuries. His attacker, aged 15, was caught soon after fleeing and arrested.
The teen later claimed to have been acting in the name of Daesh, the Arabic acronym for the Islamic State group.
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“He said several times he was acting in the name of Isis, because Muslims in France were dishonouring Islam and French soldiers were protecting Jews,” said Marseille prosecutor Brice Robin.