Italy however maintained that it allowed the ship, the Ocean Viking, to offload the migrants as most of those on board will be relocated to other European Union countries.
The move signals a change of approach to migration from the new coalition which took office on Tuesday.
Ex-Interior Minister Matteo Salvini routinely blocked access to charity-run migrant vessels.
Italian foreign minister Luigi Di Maio told Italian television that “the safe port was assigned because the European Union agreed to our request to take most of the migrants”.
But this did not mark a return to a policy of open ports, he added.
“It must be clear that, even in the past with the previous government, our goal was to ensure that those migrants who arrived in Italy were redistributed to other European countries.”
Mr Salvini, the leader of the far-right League and former ally of Mr Di Maio’s, pulled out of the coalition with his Five Star party last month in a bid to trigger new elections.
French Interior Minister Christophe Castaner tweeted on Saturday that an ad hoc European agreement had been reached between Italy, France, Germany, Portugal and Luxembourg to allow the landing. “We now need to agree on a genuine temporary European mechanism,” he added.
The EU appears to be inching towards a mechanism for this – even if it is initially a temporary, partial one.
German Interior Minister Horst Seehofer said that under the possible future agreement, his country would take 25% of rescued migrants landing in Italy. “That won’t be too much for our immigration policy,” Mr Seehofer told Saturday’s Sueddeutsche Zeitung daily.
France and Germany have each agreed to take a quarter of the boat’s migrants, with Italy to take 10%, AFP news agency reports.
People-smuggling gangs continue to make huge profits from African migrants desperate to reach Europe, as they flee war or poverty.
Most African migrants use Libya is a major transit hub to cross over to Europe.
