Italian prosecutors are investigating charges of manslaughter and “negligent shipwreck” over the sinking of a superyacht in bad weather in which UK tech entrepreneur Mike Lynch and six others died.

Ambrogio Cartosio, Italian public prosecutor in the Sicilian town of Termini Imerese, told a news conference on Saturday that the investigation was targeting “persons unknown”. But he said that could change to named individuals and would not depend on the recovery of the 540-tonne wreck of the Bayesian from the seabed near Porticello off the coast of Sicily.

“It could be that we add someone to the list of people being investigated even way before the recovery of the boat,” he said. “It seems to me likely that offences of negligent shipwreck and manslaughter have been committed. It’s about establishing who they can be ascribed to.”

Bayesian was anchored off Porticello and sank at about 4am on Monday after being hit by exceptionally violent winds. Of the 22 passengers and crew on board, 15 were rescued by a boat that had been anchored nearby, six died trapped inside the boat and another was found dead in the sea. The last body, that of Lynch’s daughter Hannah, was recovered by divers from a cabin on Friday.

Investigators found “the boat sank stern-first, not bow-first”, Cartosio said. The finding followed analysis of the position of the vessel on the seabed, interviews with survivors and the testimony of skipper Karsten Börner, whose yacht was anchored near Bayesian when the storm hit.

Börner, who rescued Bayesian survivors after they had fired a red distress flare from a life raft, told the Financial Times that he and his passengers saw something in the sea, including what seemed to be a triangle during a flash of lightning, while he worked to keep his boat in position during the storm.

“I think they saw the ship capsize and when I turned around I saw the bow, then it went down,” he said.

The stern-first sinking suggests water may have flooded into the aft, or rear, compartments of the boat, tipping its bow upwards. It is not yet known whether a large hatch in the stern just above the waterline was open and prosecutors did not comment on the issue.

The weather forecast, issued at midnight on Sunday for the 12 hours until noon on Monday, warned of isolated thunderstorms but not of any extreme weather systems, according to Admiral Raffaele Macauda of the Palermo coastguard.

But Raffaele Cammarano, deputy prosecutor, said the storm that struck the boat was “truly rapid, sudden”. He said: “From the information that we have obtained, it is more likely that it was a downburst.’’

Borner said the wind was “violent, very violent” and estimated it reached force 12 on the Beaufort scale — hurricane strength. “It was tonnes of water coming down. I never saw that before, there was a water tornado,” he added.

The prosecutors said the first five bodies to be extracted from the wreck, recovered on Wednesday and Thursday, were found in one cabin on the port side. Hannah Lynch’s body was found in another cabin on the same side.

Cammarano said the gathering of the bodies in one cabin did not necessarily indicate that the passengers were trying to escape, as they could have been pushed there by the inrushing water. “Probably they were asleep,” Cammarano commented.

Investigators said the luxury yacht gave its last position electronically at 4.06am, suggesting this was when it finally sank beneath the waves, while the survivors fired their flare from the life raft at 4.38am. Prosecutors are examining how all the crew except the chef managed to escape while all six victims whose bodies were found in the hull were passengers.

A coastguard official said a timeline for extracting the diesel from Bayesian’s fuel tanks — it can carry up to 50 tonnes — had not yet been decided. However, he said recovering the vessel from the seabed was a priority, because it would help the investigation and make the bay safer for the local community.

The vessel now lies 49 meters below the surface. Its owner will cover the costs of its recovery, according to Macuada. Records indicate that Lynch’s family owned the yacht.