A NSW police failure to conduct sexual assault examinations on a man found with a fractured skull and his underwear pulled down means there is little hope for future investigations into his death nearly 40 years ago.

William "Bill" Rooney, a Scottish man who had lived in Australia for 18 years, died six days after being found seriously injured behind a toilet block in Wollongong's CBD on Valentine's Day in 1986, a Special Commission of Inquiry into LGBTQI hate crimes was told on Thursday.

The previous night, he had been drinking at the Tattersalls Hotel with his partner Wayne Davis before they parted ways about 10pm.

Emergency services were told Mr Rooney fell off the roof of a shop before he was found in an annex behind a car park, in a space about half a metre wide.

He was wearing one shoe and sock, and appeared to have fingernail marks on his neck. TV footage showed his fly was unzipped and underwear pulled down, Counsel Assisting Meg O'Brien told the inquiry.

Six days later, the 35-year-old was declared brain dead and his life support was turned off.

No sexual assault examinations were carried out on following the incident or after Mr Rooney's death, severely impeding the chances of a homicide investigation, the inquiry heard.

About two hours after Mr Rooney was found, retailers hosed down the surrounding area, removing much of the blood and physical evidence, Detective Seargent Passmore said in an unsworn statement at the time.

The day after the attack, Mr Davis told police Mr Rooney talked with a man involved in gay bashings named Leslie John Harrison, who went under the pseudonym "Radar".

Speaking with Mr Harrison two days later, he told police he was with his girlfriend Joanne Garbutt on the night of the incident but police did not check his alibi.

Ms Garbutt has since disputed his account, telling the inquiry she was living six-and-a-half hours away in Coffs Harbour at the time.

Mr Rooney's partner later said he felt police "weren't that interested" in the case and "it was just another p**fter" during an interview with the Illawarra Mercury.

Ms O'Brien said it was puzzling that officers from Strike Force Parrabell, tasked to investigate crimes with a potential LGBTQI bias link, determined Mr Rooney's case had no evidence of homophobia.

Despite their findings, the possible involvement of convicted criminals Mr Harrison and Mark Anthony Scerri, is mentioned in seven of their 10 general comment sections, she said.

"At the very least … we submit that questions arise in relation to the coherence and rigour of the methodology of Strike Force Parrabell," she said.

She urged the inquiry to find Mr Rooney died of blunt head injuries, with insufficient evidence to establish whether it was the result of an assault or fall.

The inquiry continues on Friday and a report is due to be delivered to Governor Margaret Beazley in August.

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