Former NT police commissioner John McRoberts found guilty of attempting to pervert the course of justice

Former Northern Territory police commissioner John McRoberts has been found guilty of attempting to pervert the course of justice.

After deliberating for nine hours, a jury found McRoberts tried to "frustrate" or "deflect" a travel agent fraud investigation known as Operation Subutai between May and November 2014.

Throughout this period, McRoberts failed to disclose he was in a sexual relationship with the investigation's priority target, former Darwin travel agent and CrimeStoppers NT chairwoman Alexandra "Xana" Kamitsis.

McRoberts knew Kamitsis had become a "test case" for the investigation, which was looking into 27 travel agents suspected of defrauding the NT Health Department's pensioner travel concession scheme.

Text messages found on Kamitsis' phone after her arrest in November 2014 exposed the pair's close relationship to investigators but, when confronted at the time, McRoberts denied the relationship was anything more than "social".

The jury found McRoberts involved himself in the investigation, knowing he was "hopelessly conflicted", because he wanted stop his relationship with Kamitsis being exposed through a search warrant.

The prosecution alleged McRoberts' criminal course of conduct began in May 2014, when he raised the idea of an alternative civil approach to Operation Subutai, which was then further developed.

This approach, where travel agents suspected of fraud would be sent "letters of demand" ahead of overt criminal action, was then promoted to senior officers, the then-NT Health Department chief executive Len Notaras and ministers.

McRoberts' conduct also included frustrating the execution of a search warrant against Kamitsis in June 2014, by saying to his senior officers: "This is not ready to go to an overt investigation".

Before the jury retired, Acting Justice Dean Mildren summed up almost five weeks of evidence from senior police, former bureaucrats and ministers who served with the Country Liberals' government in 2014.

"The crown says he was in a position of conflict of interest and should not have had anything to do with the investigation into Winnellie Travel [also known as Latitude Travel], once he realised that Ms Kamitsis was the major target," he said.

Defence lawyer Anthony Elliot argued McRoberts remained involved because his deputies were seeking guidance on the "unusual" investigation, Acting Justice Mildren said.

According to Mr Elliot, McRoberts was worried about the impact of the investigation on the tourism industry and the strain on police and government resources.

Mr Elliot argued that McRoberts told senior police he was "friends" with Kamitsis but despite this, no-one asked him to step aside.

During the trial, Mr Elliot suggested that if McRoberts wanted to protect himself or Kamitsis, he could have directly ordered the search warrant in June 2014 to stop and told Kamitsis to delete all her messages.

"Do you think that she would have been the kind of person, when you look at the [text messages], that she would've been easily brushed off?" Acting Justice Mildren asked the jury.