"Some mosques are used by extremists to incite violence and only when they know that they are watched they moderate their tone," said Mustafa Mirabat, the head of the Association of Moroccan Immigrant Workers.
"All mosques in Spain should be transparent; we are not talking about private homes, but places of worship," he added.
Mirabat said his association will ask the incoming Socialist government of Jose Luis Rodriguez Zapatero to set up an Islamic Council on the model of the controversial French Council of the Muslim Faith founded in 2003, to improve communication between Muslim leaders and the state.
The French body is derided by many Muslims in the country as an organ of the state.
A spokesman for the Socialist Party declined to comment on the proposal.
Among the tasks that this council would have, Mirabat said, would be the supervision of the mosques and the appointment of Imams.
"Until now to be an Imam you just have to know the Quran and be a good person, but that's not serious," he said. He did not specify what sort regulation of Imams might be called for.
The investigation into the Madrid railway bombings on 11 March has focused on the Moroccan Islamic Combatant Group.
Thirteen of the 17 people in custody in relation with the attacks are Moroccans who were reportedly living and working in Spain.
More than 333,700 Moroccans live legally in Spain, Mirabat said. Another 200,000 are reported to have no papers, hiding from the police with jobs in agriculture or on construction sites.
The Association of Moroccan Immigrant Workers has about 14,500 members. It helps migrants get work papers, legal advice,find housing, and file complaints of police misconduct.