However, Foreign Minister Luigi Di Maio, who heads the 5-Star Movement in the governing coalition, said the boat was only being given access because other European states had agreed to take in many of those onboard.
The government formally took office on Tuesday, promising a fresh approach to migration, following the 'close-doors' policy implemented by the previous government which attracted media attention in the last years.
Italy's far-right Minister Matteo Salvini has been at the centre of global criticism for closing all Italian ports to humanitarian vessels, since his League party formed a coalition last year with the anti-establishment 5-Star Movement.
The ship, run by French charities SOS Mediterranee and Doctors Without Borders, picked up the migrants off Libya last week and had asked both Italy and Malta for permission to dock.
Recent such requests from other boats had been rejected, leaving migrants stranded at sea for prolonged periods.
"The new government is reopening the ports. Italy is going back to being Europe’s REFUGEE CAMP. (These are) abusive ministers who hate Italians," Salvini wrote on Twitter.
During his 14 months at the interior ministry, Salvini introduced rules barring rescue ships from entering Italian waters, saying Italy had borne too much responsibility for handling African migration to Europe.
Ships that defied the order risked being impounded and were threatened with fines of up to a million euros ($1.1 million).
Over the summer, the German captain of the migrant-rescue ship 'Sea Watch 3' was arrested over docking in Lampedusa along with 42 migrants onboard, defying the stringent domestic law that had closed borders to migrants.
The new government has not given details of any new system for sharing out migrants.