A security source told AFP that police arrested  11 people , while French authorities also froze the financial assets of the centre headed by Yahia Gouasmi, who is known for his anti-Zionist views and links to Iran.
The raid on Tuesday took place in the town of Grande-Synthe at 0400GMT, near the port city of Dunkirk not far from Calais on France's northern coast.
On its website (www.centre-zahra.com), the association says its purpose since its foundation in 2009 has been "to make known the message of Islam through the eyes of the Prophet and his family".
Targeting an association known as Centre Zahra France, the move included the questioning of at least 11 suspects, of which three were arrested.
"This is a counterterrorism operation," said a statement by the regional authorities.
"The activities of Centre Zahra France are under particularly close watch ... due to marked support by its leaders for movements advocating ideas contrary to the values of the (French) republic," it said.
Gouasmi has spoken in support of Lebanese Islamist group Hezbollah and the Iranian leader Ayatollah Sayed Ali Khamenei, AFP said.
Gouasmi is also the founder of the Anti-Zionist Party in France and is an associate of controversial comedian Dieudonne M'bala M'bala, a convicted anti-Semite.