The rescue on Saturday delivered one of the largest numbers of migrants to the Italian island in a single day.
Women and children were among those on board. Some of the migrants – who had been travelling across the Mediterranean Sea from Libya – reportedly displayed signs of violence.
Italian prosecutors have opened an inquiry into what may have happened.
A doctor from the humanitarian group Doctors Without Borders (MSF), Alida Serrachieri, said a number of the migrants appeared to have been physically assaulted in Libya while waiting for a boat to transport them to Europe.
Investigators are looking at the possibility that the migrants may have been falsely imprisoned in Libya, local media report.
Two coastguard vessels and a customs boat from Italy’s financial crimes police, the Guardia di Finanza, helped transport the migrants to Lampedusa.
The island’s Mayor Toto Martello described the rescue as “one of the biggest landings in recent times”.
Lampedusa is one of the main arrival ports for people wanting to reach Europe.
In May, more than 1,000 migrants landed on the Italian island in the space of a few hours.
The island has a migrant camp that was originally designed to hold fewer than 300 people. It now has more than five times that number, with many more held outside on the dusty road.
Most arrive from countries that do not qualify for asylum.