The ministry reported "three bomb alerts this morning in three school districts", without giving further details.
According to local media, the incidents occurred in the southern city of Marseille, in the eastern Jura region and in the town of Laon in the northeast, and led to evacuations.
Dozens of Italian schools received false bomb threats by email on Wednesday, leading to the evacuation of some schools, while similar threats were received by schools in the UK and Ireland.
They come after a wave of hoax bomb threats hit flights all over Europe, leading to planes being diverted to countries including France.
Asked by media on Thursday, French president Emmanuel Macron said it was "too early to say" whether the bomb threats were the work of a foreign power.
"As I speak, we do not have sufficient evidence to be able to attribute responsibility. At this stage, we cannot say that any external powers are behind these calls," he told press gathered in Dublin.
French cybercrime investigators say they believe that Iran was behind the hacking of numerous fridges at French supermarkets, which led to millions of euro of products being discarded after fridges and freezers were set to defrost mode.
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