More than 40 migrants have died in the Mediterranean today, the Italian navy said, after apparently suffocating below deck on the boat taking them to Europe.

"Operation underway... many migrants saved. At least 40 dead," the navy said on Twitter, while the Corriere della Sera newspaper said those who died were found in the hold of the vessel.

The boat, which was intercepted south of the Italian island of Lampedusa, was carrying around 300 people, the paper said.

An Italian navy helicopter spotted the boat, which was "overcrowded and starting to sink", about 21 miles off the Libyan coast, said a reporter with Italy RaiNews television at the rescue operation headquarters.

An Italian navy vessel was sent to its aid at 7 am local time and when its sailors boarded the vessel the grim discovery was made.

Survivors of the hazardous crossing from Libya often tell of how traffickers lock migrants in the hold -- most black Africans -- who pay less for the voyage.

Packed inside the confined space they not only risk drowning if the rickety boats capsize, but many also die after being overcome with diesel fumes.

The EU said yesterday that Europe was facing the worst refugee crisis since World War II.

More than 101,700 migrants have arrived in Italy by boat since the start of the year, with at least 2,040 others dying on the crossing, according to the latest figures compiled by the International Organization for Migration.