The number of missing from the vessel that sank about 60 nautical miles southeast of Lampedusa could be much greater, Francesco Galipo told AFP.
"The immigrants said there were more than 70 people aboard the boat, but we saved only 48 people. Either there are more people missing or the number given by the immigrants is not exact," he said.
The would-be immigrants were diving into the water as an Italian navy ship, La Fenice, approached to rescue the survivors.
Rescue workers pulled three bodies out of the water and were searching for other victimes, Galipo said.
Meanwhile, another boat with around 350 people aboard was spotted on Monday off Lampedusa and was being escorted to the tiny island.
A processing centre at Lampedusa, which was designed to hold some 700 people, currently counts more than 1,000, the ANSA news agency reported.
In early June at least 40 boat people perished and nearly 100 went missing after their boat sank between Libya and Italy, according to a report by the Egyptian ambassador to Tripoli.
The Libyan authorities had informed the embassy of the accident since there were Egyptians among the passengers.
Every summer sees a surge in the number of people risking the voyage aboard rickety vessels for the chance at a better life in Europe.
More than 600 people arrived in Lampedusa last Tuesday, forcing local authorities to set up an air bridge to send them on to other processing centres on the Italian mainland.
Lampedusa, some 200 kilometres south of Sicily and 300 kilometres north of Libya, is a main destination for would-be immigrants, mainly setting sail from Libya.
Rome and Tripoli signed an accord in December to set up joint patrols to fight illegal immigration, but it has yet to be implemented.