The rescuers made the gruesome discovery when they boarded a fishing boat carrying around 590 refugees and migrants to evacuate those in most distress, including two pregnant women.
The immigrants apparently died of asphyxiation, the news agencies said. It is not the first time Italian rescuers have found migrants dead on the overcrowded boats but never before were there such a large number.
The boat is being towed by the Italian navy and is expected to arrive later today in Pozzallo on the southeast coast of Sicily.
The number is expected to soar past the record 63,000 set in 2011 during the Arab Spring uprisings.
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Italy has long borne the brunt of migrants making the perilous crossing from North Africa to Europe, but EU border agency Frontex says there has been a significant rise in numbers in recent months.
The last few weeks have seen a series of tragedies, with ten people drowning and 39 having to be rescued after their boat sank off the Libyan coast earlier in June.