"In Italy, we have four mosques and over 800 places of Muslim worship," said Alfano. "We are going to close the clandestine and unregulated places, not to hamper the religion but so that it can be practised in places which are in order," he added in comments published by the local press.
The minister was speaking at a meeting in the southern town of Lecce on the subject of terrorist risks and the influence of so-called "garage Islam" - the non-registered places of worship where many of the estimated one million Muslims living in Italy go to pray.
Some of these clandestine meeting places are set up after attempts to establish a mosque through the proper channels are thwarted, often due to opposition from local officials.
"Nowhere in the world enjoys zero risk - this has been demonstrated by the dramatic timeline of terrorism from 2001 to today," Alfano said in other comments.
He added that, so far, preventative measures and intelligence-gathering in Italy had prevailed.
However Italy, and in particular Rome, are often cited as targets in Islamic State propaganda and the United States has warned the country of the risks of possible attacks.