Italian divers are said to have found the billionaire father and his daughter, 18, inside one of the sunken vessel's cabins.
The capsised ship rests 49 metres below the surface, about half a mile from the coast.
British tech tycoon Lynch was among seven people who went missing around 5 am on Monday off the port of Porticello, on the Italian island of Sicily, after a storm swamped his vessel. There were 22 people were on board the super yacht – 12 passengers and 10 crew, according to multiple reports.
The trip was reportedly intended to celebrate Lynch's acquittal in the long-running US fraud case that followed from HP's 2011 acquisition of his company, Autonomy.
Coincidentally, Lynch's co-defendant, Stephen Chamberlain, who was also acquitted, died the day of the storm after being hit by a car while out running on Saturday morning in Stretham, England. The car driver waited at the scene and is understood to be helping police with their inquiries.
Angela Bacares, Lynch's wife, was rescued at sea and is recovering.
The Independent has identified other missing individuals, such as Christopher Morvillo, a lawyer representing Lynch, and wife Neda Morvillo; Jonathan Bloomer, chairman of investment bank Morgan Stanley International; and wife Judy Bloomer.