The Northern Territory's top public servant has told the trial of former police chief John McRoberts she was annoyed when he argued criminal charges should not be pursued against travel agents, including a woman who was his lover.
Xana Kamitsis, a married travel agent and chair of Crime Stoppers NT who was having an affair with Mr McRoberts, was one of a number of agents jailed for rorting a concession scheme aimed at helping pensioners see family.
Mr McRoberts pushed for a civil rather than criminal prosecution, arguing it would be too difficult to get evidence to charge travel agents who had defrauded taxpayers of about $5 million.
Mr McRoberts has since admitted to a sexual relationship with Kamitsis but did not do so at the time, telling fellow police she was only a friend.
Jodie Ryan, the chief executive of the NT Chief Minister's Department, was head of the treasury at the time and said the travel agents' fraud was assisted by poor record-keeping by the Department of Health.
She said Mr McRoberts suggested a civil route, "which might mean writing to the travel agents saying: we understand you may have taken additional money that you shouldn't have and we have a moratorium, hand back the money and no further action would be taken".
"I was surprised by that ... I can recall at the time being a bit annoyed about the civil issue," she told the court on Tuesday.
The $5 million amount was small so merely recovering the money was not a priority, she said.
The Supreme Court jury trial of McRoberts, who has pleaded not guilty of attempting to pervert the course of justice, is in its fourth week and has heard evidence he pushed for a civil remedy and blocked a search warrant on Kamitsis' business despite a judge approving it.
He denies any wrongdoing and his lawyer, Tony Elliot, suggested to Ms Ryan he was under immense pressure to save costs due to the "perilous" state of the NT's budget and could have lost his job.
"The budget was in a difficult state (but) I can't recall a CEO losing their job because they've exceeded their budget," Ms Ryan said.
Former chief minister Adam Giles similar rejected such a suggestions by Mr Elliot earlier in the trial.