The migrants were believed to have crossed over from neighboring Turkey in speedboats, small rubber dinghies and other small boats, the Merchant Marine Ministry said. They were detained on the islet of Farmakonissi, and the larger islands of Lesvos and Samos.
Among the migrants were nine children and 23 women, the ministry said. Their nationalities were not released.
Late Thursday, authorities on Lesvos arrested a man in a speedboat, suspected of having transported 24 illegal migrants to the island.
Greece pledged this month to step up patrols in the Aegean, following a spike in arrivals of undocumented migrants - mostly from Asia and Africa - seeking a better life in the European Union.
Authorities have detained more than 6,200 migrants so far this year, compared to 3,456 in 2006.
Greece blames the problem on lax border controls in Turkey. The matter will be discussed during a visit to Greece by the Turkey's coast guard chief on Nov. 5-7.
The discovery of the submarine has unveiled a few "inconsistencies." For example, how can one explain the fact that the sub was found where it needed to be searched for from the start?