The former Northern Territory police chief John McRoberts has been found guilty of the criminal offence of attempting to pervert the course of justice.

A Supreme Court jury found McRoberts, 59, intended to "deflect" or "frustrate" the fraud investigation into his former lover, travel agent Alexandra Xana Kamitsis.

Kamitsis, a former NT Crime Stoppers boss, was the prime target of a major investigation in which numerous Darwin travel agents had been defrauding an NT government pensioner concession scheme.

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Kamitsis was jailed in 2015 for rorting taxpayers of $120,000. Detectives arrested her when McRoberts was overseas on business.

The Crown case against McRoberts was that he was conflicted and should have disclosed his relationship with her.

He instead lied about his intimate relationship while his own detectives were investigating, blocked a search warrant on Kamitsis's premises, and argued against the criminal investigation and for a civil remedy.

He engaged in what was described as other improper conduct, trying to convince politicians and bureaucrats that criminal charges would damage the tourism industry and Territory's reputation.

The court had heard intimate messages were sent between McRoberts and Kamitsis before she was arrested.

"Probably the most lonely and sad birthday I can remember but s**t happens," McRoberts says.

"Your birthday is so important to me. I'm thinking of you. Adore you BB xxxxxx," Kamitsis replies.

The jury had retired on Wednesday after Justice Dean Mildren finished summing up the trial which lasted almost six weeks.

"The accused did what he did for an improper purpose ... it was all a smokescreen," prosecutor Michael McHugh said during the trial and the jury ultimately accepted that.

It did not accept McRoberts's lawyer Tony Elliot's argument he had acted properly cautiously as a police commissioner should and had not illegally interfered with the investigation.

After nine hours deliberation the jury returned with a guilty verdict. The former commissioner faces the possibility of significant jail time.