Professor Danny Eckert breaks his silence after he clung to a Spilsby Island reef with his young son for 12 hours during Port Lincoln fishing trip tragedy that claimed the life of his father and brother

A university professor who survived with his young son by clinging to a reef for hours after their fishing boat capsized, killing three people on board, has broken his silence. 

Professor Danny Eckert, 44, and his son, 12, were on board the vessel when it was hit by a freak 6.2metre wave about 4pm Monday near Spilsby Island about 40km off the Port Lincoln coast in South Australia.

The others on board - his father Paul Eckert, 73, brother Tom Eckert, 40, and family friend Alan Bottrill, 71 - sadly died. 

Family members raised the alarm about 8.30pm after the boat did not return to Port Lincoln, sparking a search and rescue operation that found the upturned boat and winched Prof Eckert and his son to safety at 2am. 

'I wish to express my immense gratitude to the emergency responders and everyone who helped with the search and rescue efforts,' Prof Eckert said in a statement provided to the Adelaide Advertiser.

'My heartfelt thanks go to the medical staff at the Port ]Lincoln and Women's and Children's Hospitals, who have provided us with outstanding care and support.

'I extend our sincerest appreciation to everyone including the whole Port Lincoln community who have offered their help, thoughts, and prayers.'

Prof Eckert added that it was an 'unimaginably difficult time' but found comfort in the kindness friends and locals had shown. 

Prof Eckert's neighbour in Torrens Park, Adelaide, Noela Krahn, 74, said she believed he would have been holding onto his son as the pair clung to the reef in the freezing water during the night.

'He loved that boy like you wouldn't believe ... (he) would have made sure that the boy was safe,' she said. 

Tess Eckert, the wife of Tom, also spoke to the media and shared her gratitude to those who helped in the search.

The couple share two young boys, aged four and six.

'Tom was an amazing husband, father, and best friend to so many,' she said.

She added that their boys would also miss their 'Grandpapa' and shared her support for the Botterill family who she described as close friends.

Mr Bottrill's wife Pamela and their children Rónán and Amélie previously said in a statement the 71-year-old had battled cancer twice.

'Alan was 71 years old and still very much an adventurer who loved fishing, golfing and travelling with friends and family,' the statement read. 

'He leaves behind a wife, two children and two grandchildren who will miss him very much.' 

Ms Bottrill said her husband was an experienced fisherman, who 'never' imagined he'd be killed doing the hobby he loves.

She said the group had taken off in 'calm seas' on the day of the accident.

'Alan had a lifelong love of fishing and was very experienced in both boating and fishing. Our understanding is that there was a 'freak' wave that didn't allow time to activate normal safety procedures,' Ms Bottrill previously told The Advertiser.

'We have no information about what actually happened.'

Mr Bottrill and Paul had been fishing together for more than a decade after meeting while working within SA Health.

One of the pair's former colleagues, Kylie Peterson, said the duo were 'extremely adventurous' and people you'd want to 'live vicariously through'.

'Mr Bottrill was the kind of person you'd sit down and listen to and go: ''Gosh, I would love to have that spirit of adventure'',' she said.

A large-scale rescue operation for the fishermen was launched after family members alerted police just after 8.30pm on Monday when they failed to return.

As well as a police helicopter, police water operations, local Sea Rescue vessels, a Challenger jet plane and P&O cruise ship the Pacific Explorer took part in the search.

Police will now prepare reports for the coroner.

South Australia Police Superintendent Paul Bahr said Prof Eckert and his son were treated for hypothermia after they were winched to safety.

'The boat itself has also been located and is on its way back to Port Lincoln,' Supt Bahr said.

'That will be offloaded later today and will be subject to further forensic examination and any examination the coroner may require.'

Danny Eckert is a professor of Medicine and Public Health at Flinders University and the director of the school's world-leading Adelaide Institute for Sleep Health. 

He was awarded the Pierre Robin Award by the American Academy of Dental Sleep Medicine in 2019 for 'exceptional initiative and progress in the areas of education and academic research with original contributions to dental sleep medicine.'