The Mare Jonio set sail from the Sicilian port of Augusta on Wednesday.
The former tug boat is the first rescue ship to depart from Italy since the nation’s far-right interior minister Matteo Salvini closed off all ports to non-Italian vessels.
The 37-metre-long ship was bought and fitted out by the humanitarian group Mediterranea.
“This is a moral disobedience mission but also a civil obedience one,” Mediterranea’s press office said in a statement.
“We will disobey nationalism and xenophobia. Instead we will obey our constitution, international law and the law of the sea, which includes saving lives.”
The Mare Jonio is accompanied by a rescue ship run by Spanish NGO Proactiva Open Arms, and will reach the search and rescue zone on Saturday.
While the ship’s Italian flag will make it difficult for Salvini to stop it from docking in Italy, the League leader may still attempt to stop people from disembarking.
In August, Salvini left 177 people stranded on the rescue ship Diciotti for almost a week before he was forced to let them disembark at the Sicilian port of Catania.
It was among several moves made by Salvini which reflect the new government’s hardline stance against migration.