The sweep on Wednesday came a week after a migrant from Guinea stabbed a police officer outside the station. The man was later deported.
It also came two months after a police officer and soldier were stabbed by a man of Tunisian and Italian origin at the station, where many homeless people and migrants sleep rough.
Police said the blitz was aimed at combating rising crime levels in the area.
Italy is in the midst of another migrant influx, with almost 94,000 people landing on the country's southern shores so far this year, according to Italy's interior ministry, an increase of over five percent compared to the same period last year.
Many then make their way up to northern Italy in an attempt to reach countries in northern Europe, only to be left stranded at the borders with France, Switzerland and Austria due to tight immigration controls in those countries.
On Tuesday, European Commission head Jean-Claude Juncker promised Italy an extra €100 million in funding to manage the situation, on top of nearly €800 million already pledged.