A former senior police officer involved in the cold cases of gay men killed in the 1980s has told an inquiry that homophobic attacks were well-known to police.

Current and former senior police are giving evidence to a special inquiry about several strike forces, including Parrabell, Neiwand, Macnamir and Operation Taradale, that examined the cases of nearly 90 LGBTQI people found dead between 1970 and 2010.

Former detective sergeant Stephen Page, who commanded Operation Taradale in 2002, entered the witness box on Tuesday.

Answering Senior Counsel Assisting Peter Gray's pointed questions with short and sharp replies, Mr Page said there were shortcomings in initial police investigations of gay men reportedly killed.

"There should have been alarm bells that there was a problem with assaults on gay men in that era (and) in that area," Mr Page told the inquiry.

"It was prevalent and well-known to police."

Operation Taradale investigated the disappearance and suspected deaths of three gay men - Ross Warren, John Russell and French national Giles Mattaini - in the 1980s in Bondi.

Mr Page also worked with the family of US mathematician Scott Johnson, who was found dead at the bottom of cliffs at Manly in northern Sydney in 1988.

His death was initially ruled a suicide, only for police to reopen the case in 2012 after pressure from his family.

In the NSW Supreme Court last Thursday, Scott White pleaded guilty to Mr Johnson's manslaughter.

The inquiry has previously heard throwing gay men off cliffs near "beats" was a common tactic among assailants.

Competing investigations shifted responsibility and assigned blame to certain officers, including Mr Page, without getting to the bottom of how these men were killed, the witness said.

Mr Page rejected the characterisation by covert operation Neiwand that Taradale had "tunnel vision".

"You're aware that Neiwand ... accuses you of deliberately withholding evidence from the coroner, is that true?" Mr Gray asked.

"No," Mr Page replied.

"My reputation was absolutely and professionally destroyed ... it feels like I wasted a lot of time with Taradale.

"A lot of the gains we had along the way were almost for nothing."

However, Mr Page also recounted how professional jealousy among police ranks had driven him away from further investigating these deaths.

"I was pushed out of the way so that there could be a free swing at the families, or more the deceased," he told the inquiry.

Later in the hearing, Flinders University's Dr Derek Dalton, who was part of an academic review team examining Strike Force Parabell's work, took the stand.

Parrabell was established in 2015 to review 88 deaths that occurred between 1976 and 2000, motivated by a potential gay-hate bias.

Mr Gray said there was a close relationship between the police and Flinders University researchers that could have influenced the decision to choose interstate academics, instead of Sydney-based experts.

But under questioning from Mr Gray, Dr Dalton bristled at the suggestion that he was a "police apologist".

"We were in South Australia so we were not totally embroiled in the animosity that has long existed between NSW Police and the gay community, which I don't think is any great secret," he said.

The afternoon session on Tuesday began with Dr Dalton making reference to a scene from the US comedy series Seinfeld to disguise his nervousness, but hours later he was shedding tears while defending his academic credentials.

"It (the hearing) has been a poisoned chalice from the second I started," a tearful Dr Dalton said.

"I was immediately constructed as a police apologist. It's a disgusting thing. I'm not a police apologist.

"I've spent years of my life documenting hate against gay people, and to be constructed as such is a despicable thing.

"That's what I feel is happening today," a visibly distressed Dr Dalton told Mr Gray, before Commissioner John Sackar quickly adjourned the hearing.

The inquiry continues on Friday.