The cell was active in the north of Morocco, where Spain retains two sovereign enclaves, and around Marrakesh in the south, the ministry said in statement carried by the MAP national news agency.
The ministry did not identify the alleged leader of the cell nor specify how many arrests had been made. It said the suspects would be brought to trial after the investigation had been completed.
Morocco has announced the dismantling of several alleged jihadist cells in recent months.
Al-Qaeda in the Islamic Maghreb, the network's North Africa affiliate, released a video in September calling for jihad in Morocco, which it referred to as a "kingdom of corruption and despotism".