The identities of the victims were not immediately given by the authorities. Three of the bodies were brought ashore and taken to nearby hospitals for formal identification on Wednesday. The fourth body was being taken to land as evening set in.
Britain's Daily Telegraph reported that two of the dead were Lynch and his 18-year-old daughter Hannah. Local authorities in Sicily declined to comment on the report.
The British-flagged Bayesian, a 56-metre-long (184-foot) superyacht was carrying 22 people and anchored off the port of Porticello when it was hit by a fierce, pre-dawn storm on Monday.
Lynch, 59, was one of Britain's best-known tech entrepreneurs and had invited friends to join him on the yacht to celebrate his recent acquittal in a fraud trial in the United States.
Besides Lynch and his daughter, the other people unaccounted for after the disaster were Judy and Jonathan Bloomer, a non-executive chair of Morgan Stanley International; and Clifford Chance lawyer Chris Morvillo and his wife Neda Morvillo.
Specialist rescuers have been searching inside the hull of the sunken yacht for the past two days. The victims were believed to have been trapped in cabins, which have proved extremely hard to get to, with divers only able to stay in the vessel for 8 to 10 minutes before having to re-surface.
Fifteen people managed to escape the yacht before it capsized in the pre-dawn tempest, while the body of the onboard chef, Canadian-Antiguan national Recaldo Thomas, was found near the wreck hours after the disaster.
Two New Zealanders, lawyer Ayla Ronald who is based in the United Kingdom, and the yacht's captain James Cutfield, were among those rescued.
Cutfield, a 51-year-old New Zealander who survived the shipwreck, was a "very good sailor" and "very well respected" in the Mediterranean, his brother Mark told The New Zealand Herald.
MYSTERY
The Bayesian is lying on its side at a depth of around 50 metres, apparently largely intact.
Besides the diving team, the coast guard has deployed a remotely operated vehicle to scan the seabed and take underwater pictures and videos that it said may provide "useful and timely elements" for prosecutors looking into the disaster.
The coast guard has been questioning survivors, including the captain of the Bayesian, and passengers on the yacht that was moored next to it who witnessed the ship going down, judicial sources said.
No one is under investigation at the moment, sources added.
Experts have been at a loss to explain how a large luxury vessel, presumed to have top-class fittings and safety features, could have sunk within minutes, as recounted by witnesses. The yacht anchored next to it was unharmed by the storm.
The Bayesian, which was owned by Lynch's wife, was built by Italian shipbuilder Perini in 2008 and last refitted in 2020. It had the world's tallest aluminium mast, measuring 72 metres, according to its makers.
Lynch has been referred to as Britain's Bill Gates. He built the UK's largest software firm, Autonomy, which was sold to HP for $11 billion in 2011, after which the deal spectacularly unravelled with the U.S. tech giant accusing him of fraud, resulting in a lengthy trial.
He was acquitted on all charges by a jury in San Francisco in June. Morvillo had represented him at the trial, while Bloomer was a character witness on his behalf.
Matthew Schanck, chair of the Maritime Search and Rescue Council, a United Kingdom-based non-profit organisation that trains sea rescuers, said the Bayesian was the victim of a "high impact" weather-related incident.
"If it was a water spout, which it appears to be, it's what I would class as like a black swan event," he told Reuters, meaning a rare and unpredictable phenomenon.