Attempts to launch trial proceedings against the far-right League for blocking migrants aboard another ship earlier this year fell through after the Senate ruled he should not be stripped of his parliamentary protection to face charges.
"I am under investigation once again for 'false imprisonment'," Salvini said on Twitter.
"I don't know whether to laugh about it or not," he said, insisting that his policy of closing Italy's port to people attempting the perilous crossing from Libya to Italy still stands.
The latest probe centres on 47 people rescued on January 19 off Libya by the ship Sea Watch 3, owned by a German charity and flying a Dutch flag, which was only permitted to dock on January 31 after Italy struck a deal with other European countries to take in the migrants.
Prosecutors in the Sicilian port city of Syracuse, where the ship took shelter from bad weather between January 24 and 30, have opened an investigation into alleged false imprisonment and named the minister as the suspected perpetrator.
Palermo mayor Leoluca Orlando, who in January had offered to allow the Sea Watch ship to berth, said he hoped that Salvini would "not be tempted to try to dodge justice once more with the odious recourse to parliamentary immunity".
The probe earlier this year related to the rescue in August of 190 people by Italy's Diciotti coast guard ship, who were left stuck at sea for 10 days without permission to dock.