Twenty-three of the 70 migrants, mostly from north Africa, Eritrea and Ethiophia, staying at the Baobab centre near Tiburtina station were detained, La Stampa reported.
Some 60 police officers, surrounded by sniffer dogs, arrived at the centre in armoured vehicles at around 6.30am.
Baobab, which is run by dozens of volunteers, is mostly used by migrants transiting through the capital before making their way to northern Europe and has often been at the centre of refugee solidarity efforts.
“We suspect that the controls today were related to public order needs and are part of the response to the Paris attacks,” one of the volunteers was quoted by La Stampa as saying.
One of the Paris attackers allegedly posed as a refugee, who entered Europe through the Greek island of Leros using a fake Syrian passport.
Volunteers expressed concern that the centre might soon be cleared, but without any back-up accommodation plan for the people living there.
The area outside Tiburtina station also hit the headlines in June when over 100 transiting migrants formed a makeshift camp after Baobab, which housed some 800 people at the time, exceeded capacity.
The security crackdown also comes less than a week after two Syrians were arrested for allegedly attempting to travel from Bergamo to Malta on false passports.
Meanwhile, it emerged on Monday that Salah Abdeslam, who is still being hunted over his alleged involvement in the Paris attacks, travelled through Italy in August.