Dozens of people are feared to have drowned in the second shipwreck in as many days in the southern Mediterranean, amid tentative signs that some Syrians may be trying once again to make for Europe from Libya.

At least 20 people drowned in a wreck 35 nautical miles north of the Libyan smuggling hub of Zuwara when a repurposed fishing boat sank on Thursday morning, the EU’s anti-smuggling operation said. Photographs taken from an EU reconnaissance plane showed groups of men desperately waving at the aircraft from a half-submerged blue trawler.

It followed another tragedy on Wednesday, when a boat of about 600 sank in nearby waters, drowning at least five.

Thursday’s death toll may be far higher, said a spokesman for the EU’s Operation Sophia, whose ships and planes were involved in the second rescue. “We can estimate that at least 20 or 30 have died, but we don’t know the final numbers,” said Captain Antonello de Renzis Sonnino. “The operation is still ongoing.”

@EUNAVFORMED_OHQ #opSophia the @Armada_esp frigate #ReinaSofia now rescuing these #migrants spotted by #SW3Merlin3 aircraft...

The boat may be the same sinking vessel that was detected earlier in the day by Alarm Phone, a group of Europe-based activists who take calls from stricken asylum seekers and refer their coordinates to coastguards.

Alarm Phone took a call at 8.45am CET from a boat of refugees in waters north of Zuwara, reporting that a second boat was sinking nearby, though the group said: “It is difficult for us to know for sure that this is the same shipwreck.” Nevertheless, the group believes those they spoke to were Syrian – the first sign since the start of the EU-Turkey deal that Syrians are beginning to use Libya as springboard to Europe.

An activist with Alarm Phone said: “The guy we were speaking to was Syrian, and he said that most of the people on the boat were Syrians and Iraqis. The people around him were talking in a Syrian dialect, mostly north-eastern Syria. Additionally, we are monitoring Facebook pages in Arabic and we are witnessing lately that there are a lot of people arriving in Libya and willing to go to Europe.”

If confirmed, the news would suggest that Syrians have started to think of alternative ways to reach northern Europe after the EU-Turkey deal made it harder for people to get there via the Balkans.

Facebook posts seen by the Guardian suggest that smugglers are encouraging Syrians to make their way to Libya via Sudan. “Announcement to all Syrians and Sudanese,” reads one post on a secret group called Migration to Libya. “The Sudan–Libya desert route is back to business, costing US$1200 from Khartoum to Tripoli.” The smuggler left a Libyan phone number on the post, and said the onwards trip to Italy would cost $1000.

Syrians formed the largest proportion of people using the Libya-Italy migration route in 2014 but largely abandoned the route in 2015 when it became much easier to get to Europe via Greece.

Migration experts expected Syrians to shift back to Libya following the EU-Turkey deal in March, but until this week the flow to Italy has almost exclusively been driven by people from sub-Saharan Africa.

In a separate development, a leaking hull and the sudden movement of passengers were confirmed as the main causes of a shipwreck that left more than 550 people fighting for their lives in the Mediterranean on Wednesday, according to the navy captain who rescued them.

Italian navy rescues 500 refugees after boat capsizes – video

Dramatic photographs taken by an Italian naval crew showed the boat capsize on Wednesday, tossing hundreds of mainly sub-Saharan Africans into the sea.

The captain of the naval boat said the capsize happened once panicked passengers moved towards the side of their vessel, frightened of being stuck on a leaking boat, and hopeful of getting rescued first.

Captain Francesco Iavazzo said: “I tried to keep the people calm, saying: ‘Please sit down, do not stand, do not walk, because the boat isn’t stable.’ But fear is fear, so the people were not listening. The boat was already taking in water, so the stability was even worse.”

Speaking to BBC Radio 4’s Today programme, Iavazzo added: “At a certain point it capsized. All I did was take my ship as close as possible to the wreck and order my crew to throw into the water everything that could float, to give people something to hold on to.”

An experienced captain, Iavazzo said the drama had shocked him and his crew. “I never saw myself in a situation of this magnitude,” he said. “When something like that happens, it touches you inside. You would like to save everybody, to magically push them out of the water at once. Then you crash with reality. But we did all that was possible to be done.”

At the final count, 562 people were saved from the wreck, with five bodies found. More may have drowned. “We can’t exclude the fact that more people were [trapped] inside the ship,” he said.

The rescued people were due to be brought to Porto Empedocle, a small port on the Sicilian coast, at 1pm BST on Thursday afternoon.

Their stricken ship was the latest of at least 38 smuggling missions to be rescued in the southern Mediterranean since the start of the week. More than 6,000 lives have been saved since Monday, 11,000 since the start of the month, and 39,000 since the start of the year, according to the International Organisation for Migration.

This puts the rate of arrivals to Italy at roughly the same level as last year, when 39,000 had arrived by 26 May, and 47,000 by the end of the month. While the fragile EU-Turkey deportation deal has – for now – drastically reduced migration numbers to Greece, this has not yet sparked an increase in people trying to reach Europe via Libya and Italy.

After being rescued in the southern Mediterranean, people are taken to Italy and then usually told to leave within seven days. In order to stop their onward movement through Europe, Austria, Italy’s northern neighbour, recently changed its laws so that people can no longer apply for asylum at the border.

Other European politicians, including David Cameron, have suggested sending asylum seekers straight back to Libya – even though it is a warzone where many refugees are subject to what amounts to modern-day slavery.