The woman is now on trial for making false accusations to police about two rapes. She claimed the first occurred in 2007 when she was a teenager, at the hands of her neighbour.

The second, she had alleged, had occurred at the hands of her ex-boyfriend, an Alexander Maconochie Centre guard who was locked up on remand in Goulburn for four months.

The woman was working for NSW police at the time, and was living with her new boyfriend, who was a NSW police officer.

Gungahlin police, led by Acting Sergeant Scott Corcoran, were investigating her allegations of physical and sexual abuse.

But their colleagues in the criminal investigations area had suspicions about the truth of her claims, and had taken over the investigation and secretly set up covert surveillance to test the allegations.

Mr Corcoran, who is no longer with ACT Policing, gave evidence for much of Wednesday in the ACT Magistrates Court.

He had investigated the woman's allegations for six months and said he "absolutely" believed her and would not have brought a prosecution in bad faith.

At one point, prosecutor Anthony Williamson asked whether he was embarrassed about the case. That question was objected to and was not answered.

Mr Corcoran's evidence suggested deep tensions between him and his criminal investigations colleagues.

He said the relationships between the two areas, and between criminal investigations and the woman making the allegations, had deteriorated.

"Things were very difficult," he said.

Mr Corcoran said his team was blocked from accessing the case on the police records management system, something he believes was done by criminal investigations detectives.

He told defence lawyer Michael Kukulies-Smith of one "very terse" moment, which occurred when he had responded to a call from the woman at her Bonner home.

He said he went to the scene, but got a phone call from a criminal investigations detective, Senior Constable Leesa Alexander, who he claims said:

"[She said] 'don't f---ing touch anything. Don't talk to the victim. There's someone coming out there'."

"Seeing as at the time she was a senior constable and I was an acting sergeant, I found it a little inappropriate."

He said the conversation made him realise they were treating the woman that he believed to be the victim, as the suspect.

But he said he had no idea there was any issue with his brief of evidence until the prison guard was freed from Goulburn jail, following a bail hearing in which serious concerns were raised about the woman's credibility. The entire prosecution against the guard later collapsed.

Mr Corcoran said that when criminal investigations had taken over the case, Detective Senior Constable Alexander had asked him whether he believed the woman's claims.

He said he found that question alarming and something he'd never been asked before.

"I would say it's extraordinary," he said.

"I found it extraordinary. The whole situation was extraordinary."

During the investigation, Mr Corcoran said he gave the woman his personal mobile number, something he said was not unusual.

He said he personally installed a GPS device and duress alarm on her car, and set it up to send a text to his personal phone, her boyfriend's phone, and the Gungahlin duty sergeant when she was in trouble.

Mr Corcoran used his corporate credit card to buy the GPS device from a retail store, equipping it with a sim card registered to his personal name, rather than to the Australian Federal Police, because of significant "red tape".

He said the woman had never expressed a desire to use the criminal allegations in family law proceedings involving her ex-boyfriend.

The hearing continues before Chief Magistrate Lorraine Walker on Thursday.