Former NT Police Chief John McRoberts has appeared in court charged in relation to an investigation of a now-jailed travel agent he allegedly had a relationship with.

The case against McRoberts, 59, who was in Perth and whose lawyer telephoned into the Darwin Local Court for the hearing, was adjourned until July.

McRoberts is charged with perverting the course of justice in relation to the investigation involving Darwin travel agent Xana Kamitsis.

He has previously denied any wrongdoing in the matter.

Kamitsis, who was also chair of CrimeStoppers NT, was jailed in December 2015 for defrauding a government pensioner travel concession scheme of about $110,000.

During Kamitsis' trial the court heard she had had an intimate relationship with McRoberts and another senior police officer.

Victorian special prosecutor Lesley Taylor, who investigated McRoberts, is acting as prosecutor in the matter while WA barrister Tony Elliott is representing him.

Ms Taylor had been handed a brief of the investigation into McRoberts by the Australian Federal Police last year.

The matter was adjourned until July 6, with Judge Michael Carey excusing McRoberts from personally having to appear at that hearing.

McRoberts was the NT police commissioner for five years until January 2015, and prior to that was the former assistant commissioner of WA Police, between August 2004 and December 2009.

He faces a maximum of 15 years in prison if found guilty of perverting the course of justice, with police alleging the offence took place between May 7 and November 14 in 2014.

Kamitsis was arrested at her workplace on November 14, 2014 in relation to her fraud charges.

McRoberts was succeeded as NT police commissioner by Reece Kershaw, who was elevated to the top job in April last year.