He said Sea-Watch 3, which had not been given permission to dock, had put at risk tax police by squashing one of their motor launches against the port front as it tried to stop the docking.
Salvini, who criticised the Netherlands saying it had given the ship a flag and then washed its hands of the matter, told RAI radio that Italy had been given assurances by five European countries they would take the migrants.
He did not name the countries but media reports said France, Germany, Luxembourg, Finland and Portugal had agreed.
Speaking at the G20 summit in Osaka, Premier Giuseppe Conte said that, as a lawyer, he recognised there were grounds for possible criminal charges but said it was up to judges to apply the law. "But laws are laws whether you like them or not," he said.
Rackete, who has become a symbol of defiance for challenging Salvini's authority, is already under investigation for breaking Italy's beefed up laws against non-government rescue ships.
A Foreign Office source said on Saturday under Italian laws Sea-Watch 3 would be seized, adding it faced a fine of 20,000 euros ($22,700) which, if not paid, could reach 50,000 euros.