A fishing boat containing the bodies of about 30 people was being towed by an Italian navy frigate to the Sicilian port of Pozzallo in the latesttragedy to hit the busy Mediterranean crossing route.

The Italian navy said the bodies had been found in the bow during a rescue mission on Sunday afternoon as part of the country’s Mare Nostrum (Our Sea) operation, which aims to intercept migrant vessels before they run into trouble.

The probable cause of death was asphyxiation and drowning, according to medical staff at the scene, who also advised against the bodies being removed “due to restricted space”, a navy statement said on Monday.

Once the navy had finished

the 566 survivors on to the Grecale, the frigate began towing the boat to Pozzallo, a small port on the south-east coast of Sicily, where it is expected to arrive on Tuesday.

Although the Italian government would like other EU countries to help shoulder its €9m(£7.2m) monthly costs, Rome is committed to the Mare Nostrum operation, which it and non-governmental organisations say has saved countless lives.

The operation was launched in the aftermath of twin disasters in October, in which about 400 people died.

But as the discovery on Sunday shows, the mission has not managed to prevent deaths. In May, 36 people died and 42 were missing after their boat ran into trouble off Libya, while at least 17 more died when their vessel sank south of the Italian island of Lampedusa.

The tragedies have prompted rightwing political critics of Mare Nostrum to demand an end to the operation, arguing that it has simply encouraged more people to make the perilous crossing.

Matteo Salvini, the leader of the xenophobic Northern League, accused the prime minister, Matteo Renzi, of having blood on his hands following the latest tragedy.

“Another 30 dead on a boat. Another 30 dead on the consciences of those who defend Mare Lorum [Their Sea]. Stop the departures, help them in their own countries, immediately,” he wrote on Facebook.

After a busy weekend in which the navy said more than 5,000 migrants and asylum seekers had been rescued, the pressure looked certain to be raised on southern Italy’s already overstretched ports and reception facilities.

Last Thursday the interior ministry said almost 60,000 people – including more than 10,000 Syrians – had arrived in Italy by sea this year.

Although there are not yet official figures, the weekend’s arrivals would appear to indicate that, in the first half of this year, as many migrants andrefugees have arrived in Italy by sea as came in the whole of 2011, which had held the record for the number of arrivals.

Local authorities in Sicily remain broadly supportive of Mare Nostrum, but are pleading for more resources. As the Grecale headed towards Pozzallo, the town’s mayor, Luigi Ammatuna, was quoted as saying the latest tragedy was “an emergency that we cannot tackle alone”.

He reportedly raised the alarm over how the bodies would be treated once on land, owing to a lack of spaces in Pozzallo’s morgue, already taken up by two migrants awaiting burial.

The navy said on Monday that, as well as the Grecale, the Chimera, a navy corvette, was due to dock in Pozzallo with 353 migrants on board.

The navy ship Orione and merchant ship Mare Atlantic were due to come into the port of Messina, in north-east Sicily, with 396 and 235 on board respectively.

The Dattilo, a coastguard vessel, was due to dock at the port of Augusta with 1,096 people on board, the navy added.

The Etna was carrying 1,044 migrants to Salerno on the Italian mainland and the San Giorgio was heading to the Puglian city of Taranto with 1,170 people on board.

Two merchant ships were taking 295 people to Trapani, on the west coast of Sicily. Porto Empedocle, on the south coast of the island, was due to receive 341 migrants and refugees being taken to safety by the coastguard.