The British-flagged "Bayesian", a 56-metre-long (184-ft) sailboat, was carrying 22 people and was anchored just off shore near the port of Porticello when it was hit by ferocious weather, the Italian coast guard said in a statement.
Eyewitnesses said the yacht vanished quickly beneath the waves shortly before dawn. Fifteen people escaped before it went down, including Lynch's wife, Angela Bacares, who owned the boat, and a one-year-old girl.
The names of the dead and missing were not immediately released, but a person familiar with the rescue operation confirmed that Lynch and his 18-year-old daughter, Hannah, were not accounted for.
Salvatore Cocina, head of the Civil Protection in Sicily said Jonathan Bloomer, chairman of Morgan Stanley International MS.N and Chris Morvillo, a lawyer at Clifford Chance were also among the missing people.
Italian media said the dead man was the yacht's onboard chef.
Morgan Stanley did not immediately respond to a phone call and email seeking comment after hours. Clifford Chance did not return a request for comment.
The Italian coast guard said the missing had British, American and Canadian nationalities. Survivors said the trip had been organised by Lynch for his work colleagues.
"The wind was very strong. Bad weather was expected, but not of this magnitude," a coast guard official in the Sicilian capital Palermo told Reuters.
The captain of a nearby boat told Reuters that when the winds surged, he had turned on the engine to keep control of his vessel and avoid a collision with the Bayesian, which had been anchored alongside him.
"We managed to keep the ship in position and after the storm was over, we noticed that the ship behind us was gone," Karsten Borner told journalists. The other boat "went flat on the water, and then down," he added.
He said his crew then found some of the survivors on a life raft - including a baby girl and her mother - and took them on board before the coast guard picked them up.
Lynch, aged 59, is one of Britain's best-known tech entrepreneurs. He built the country's largest software firm, Autonomy, from his ground-breaking research at Cambridge University, and became known as Britain's Bill Gates.
He sold the firm to HP for $11 billion in 2011, before the deal unravelled spectacularly following the acquisition, with the U.S. tech giant accusing him of fraud.
Once lauded by academics, scientists and politicians, Lynch spent much of the last decade in court defending his name. He was acquitted by a jury in San Francisco in June, after he spent more than a year living effectively under house arrest.
He said at the time that he was "elated" to be cleared in the criminal trial in which he denied any wrongdoing and blamed HP for botching the integration of the two companies.
DIVERS INSPECT WRECK
The coast guard said divers were inspecting the wreck of the Bayesian, which was lying at a depth of 49 metres.
Prosecutors in the nearby town of Termini Imerese have opened an investigation to look into what had gone wrong.
Storms and heavy rainfall have swept down Italy in recent days after weeks of scorching heat, which had lifted the temperature of the Mediterranean sea to record levels, raising the risk of extreme weather conditions, experts said.
"The sea surface temperature around Sicily was around 30 degrees Celsius (86 Fahrenheit), which is almost 3 degrees more than normal. This creates an enormous source of energy that contributes to these storms," said meteorologist Luca Mercalli.
"We can't say that this is all due to global warming but we can say that it has an amplifying effect," he told Reuters.
The Bayesian was built by Italian shipbuilder Perini in 2008 and was last refitted in 2020. Its 75-metre mast is the tallest aluminium mast in the world, Perini said on its website.
The shipspotting.com website said the boat was owned by a firm called Revtom Limited. Lynch's wife Bacares is named as the sole shareholder of the firm on company documents.
The yacht's name would resonate with Lynch because his PhD thesis and the software that made his fortune was based on Bayesian theory.
The ship won a string of awards for its design and can accommodate up to 12 guests in six suites and a crew of 10, according to online specialist yacht sites.
The boat left the Sicilian port of Milazzo on Aug. 14 and was last tracked east of Palermo on Sunday evening, with a navigation status of "at anchor", according to vessel tracking app Vesselfinder.
