Roman Quaedvlieg has been on leave for nine months amid an internal investigation into allegations he helped a junior staffer, with whom he had a relationship, secure work at Sydney airport.

Mr Quaedvlieg, who is estimated to have accrued close to $500,000 in salary payments while on leave, has denied the allegations against him.

The home affairs minister would not comment on whether the investigation was complete but defended the time it had taken.

"Necessarily these matters are protracted," Mr Dutton told the National Press Club on Wednesday.

"Because if there is a discovery of a piece of information, a document, a question needs to be asked, there is a natural justice process that needs to be adhered to and you would expect nothing less."

Mr Dutton said government lawyers would always err on the side of caution in allowing people to respond.

"I wouldn't seek to interfere in a legal process, deny someone natural justice or draw conclusions ahead of the appropriate time. That will follow its course and we'll have a comment to make on that in due course," he said.

He praised the efforts of acting ABF commissioner Michael Outram, who he said was doing an outstanding job.

"I've spoken to some of the results within the border protection side of the portfolio. That's continued uninterrupted," Mr Dutton said.

Australian Associated Press