The patrol vessel Cigala Fulgosi came to the migrants' aid Thursday after the engine on their inflatable boat failed in worsening weather. Only a few of them had lifejackets.
It is the first time a marine vessel has been forced to take migrants it rescued in the southern Mediterranean, off the Italian island of Lampedusa, further north to land them there.
The decision came from the far-right, anti-migrant Interior Minister Matteo Salvini who had regularly expressed his frustration at the actions of Defence Minister Elisabetta Trenta.
Trenta, a member of coalition partners the Five Star Movement does not share Salvini's hard line on migrants.
While they will land in Genoa, Salvini said Friday: “No foreigner will stay in Liguria (the Genoa region) or at the expense of Italian tax-payers.”
Since he came to power a year ago, Salvini has often blocked the work of rescue boats in the Mediterranean and scaled back Italian navy patrols in the region.
The Cigala Fulgosi was at sea to provide security for oil platforms and fishing vessels off the coast of Libya.