The special commission of inquiry, in its second block of hearings, is probing the police approach to suspected hate crimes against LGBTQI people between 1970 and 2010.
Of particular focus is NSW Police Force's Strike Force Parrabell, a three-year review of 88 deaths of LGBTQI members from 1976 to 2000.
Its final report in 2018 concluded 23 deaths remained unsolved.
Counsel Assisting Peter Gray pressed senior police officer Anthony Crandell on Thursday on the "validity" of Parrabell's methodology, saying "perhaps it was compromised".
Mr Gray said an independent academic review by Flinders University researchers had found holes in the Parrabell report published in 2018.
But Mr Crandell rejected this, saying the Bias Crime Indictors, a tool to determine whether hate crimes have occurred, were solid.
"I thought our methodology was sound and the comment that it hadn't been researched or validated before was something I couldn't do anything about," he said.
Commissioner Judge John Sackar interjected, saying: "let's not mince words".
"You know they (the academics) invented their own methodology for the very reason that they couldn't anoint and accommodate yours," he said.
Mr Crandell replied "yes".
"Did it not occur to you then that maybe the whole exercise (Parrabell) had been misguided?," Mr Gray continued.
Mr Crandell said he still believed the research tools used were "valid and appropriate".
"By the time the researchers had conducted their review, it was late in the piece," he said.
The inquiry also heard how the police taskforce did not explicitly share its research techniques with leading Sydney-based LGBTIQ rights organisation ACON.
"On reflection, do you think it would have been a good thing to do that?," Mr Gray said.
"I could have done that I guess," Mr Crandell said.
The inquiry resumes on Friday.
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