Carola Rackete was arrested at the Italian port of Lampedusa after a two-week stand-off with police at sea.
Her vessel, Sea-Watch 3, was banned from docking, but it eventually entered the port on Friday night.
On Saturday, Mr Salvini called Ms Rackete a “rich, white, German woman” who had committed “an act of war”.
“She tried to sink a police launch with officers on board at night,” he said. “They say ‘we’re saving lives’, but they risked killing these human beings who were doing their job, it’s clear from the videos.”
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Mr Salvini added: “A vessel weighing hundreds of tonnes tried to ram… a police launch with officers aboard, who managed to get out of the way to save their lives. That’s a criminal act, an act of war.”
Ms Rackete could face a 10-year jail term if convicted of attacking a police boat.
She had rescued 53 migrants off the coast of Libya on 12 June, who were drifting on an inflatable raft in the Mediterranean sea.
Mr Salvini wants clarity on “numbers, timelines and means” before he allows them off the ship, interior ministry sources told AFP news agency.
He previously said the migrants could only disembark if they headed straight to the Netherlands, where the Sea-Watch 3 is registered, or to Germany.
Ms Rackete said Sea-Watch had tried to co-operate with the authorities, engaging with Italy, Germany, Malta and France and opening contacts with the European Commission.
However, after two weeks in limbo, the German charity Sea-Watch said the boat was forced to enter Italian waters, as there was no other option left to ensure the migrants’ safety.
Who is Carola Rackete?
The “rich, white, German woman” who riled Mr Salvini has a nautical degree and studied environmental sciences in the UK.
The 31-year-old has taken part in expeditions, both for research organisations and for the environmental group Greenpeace.
Ms Rackete later joined Sea Watch, a non-governmental association that carries out rescue missions in the Mediterranean.
Now a left-wing hero, she has very little social media presence, except for posting video updates of the rescue mission on Twitter in recent weeks.
In the latest one, she said: “I have decided to enter the harbour, which is free at night, on my own.”
Sea Watch chairman Johannes Bayer expressed support for Ms Rackete’s actions and tweeted that he was “proud of our captain”.