But Australian Federal Police Detective Superintendent Scott Moller said investigators were dedicated and hard-working nonetheless.
He revealed he is a survivor of sexual assault and this motivated him to join the police force and help other victims of the crime.
Supt Moller was the lead officer who investigated Brittany Higgins' allegation her former colleague Bruce Lehrmann raped her in 2019, inside the Parliament House office of then coalition minister Linda Reynolds after a night out.
Mr Lehrmann denies the allegation.
He said officers in the territory's sexual assault and child abuse team (SACAT) were very young and inexperienced and said few had undertaken special sexual assault training.
But he said investigators who examined Ms Higgins allegations were "extremely professional" and "put their heart and soul into gathering as much evidence as they could".
AFP Senior Constable Emma Frizzell, a member of the SACAT team who investigated Ms Higgins' complaint, and Commander Michael Chew will give evidence to an independent inquiry on Thursday.
The inquiry is examining how the territory justice system handled the high-profile case.
Supt Moller said the SACAT team was "a training ground for budding detectives" to learn their investigative strategies.
"The training (officers) are given at the moment is learned on the job," he said on Wednesday.
While the organisation took pride in the fact that the division was used to provide training, he said it also presented challenges.
"We've depleted the experience to an extent where we have very young officers running investigations with minimal or less than ideal direction from a senior officer," he said.
Supt Moller said he was proud of his officers for pursuing Mr Lehrmann's prosecution despite holding personal beliefs there was not enough evidence to charge him.
While he originally thought there was not enough evidence, Supt Moller said his opinion changed when he read advice from Director of Public Prosecutions Shane Drumgold that the prosecution should go ahead.
But he would not concede that his original view of the case was wrong or that investigators had lost their objectivity.
"I would say (investigators) had deeply seated views in relation to not having sufficient evidence and even though they had those views, they pushed forward against their own beliefs," he said.
"Their opinions were highly held, and I'm not stepping away from that, I'm actually proud of them for having those opinions.
"But what I'm more proud of is they moved forward against their own opinions, they followed the process and moved forward with the prosecution."
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