The Border Force commissioner Roman Quaedvlieg has been sacked for misbehaviour after a nine-month disciplinary investigation.

In a statement on Thursday the government confirmed the governor general had sacked Quaedvlieg on the government’s advice, listing several grounds for dismissal including failing to disclose a change in his relationship status and modifying policies to advantage a candidate for recruitment.

Quaedvlieg has reportedly been absent since 25 May and the government confirmed in July that the Border Force head was on leave due to an external probe into the disciplinary matter.

Reports said Quaedvlieg was investigated by the Australian commissioner for Law Enforcement Integrity over allegations he helped get a job at Sydney Airport for a junior staff member with whom he was in a relationship.

The statement said Quaedvlieg had engaged in “acts and made omissions” which materially advantaged the candidate, which was inconsistent with an oath he took to hold the role.

It said he failed to disclose a “significant change in his personal life” and made a “wilfully or recklessly false statement” about his relationship status to the immigration minister. Quaedvlieg also failed to disclose that he had an interest in the candidate securing the position.

The statement described the sacking as “extremely unfortunate” given his “long and conspicuous public service”.

“However, the relevant conduct went beyond an isolated error of judgment and ultimately undermined his capacity to continue in the office of ABF commissioner.”

Before the sacking Quaedvlieg had continued on paid leave on a salary of $618,000 a year during the investigation over allegations which he has always strenuously denied.

Following the announcement of his sacking, Quaedvlieg issued a statement maintaining his innocence, and strongly hinting he would seek an unfair dismissal claim. He said he had not been given a chance to see the government’s statement before it was tabled.

“I have consistently maintained my strong denial of those particularised grounds over the lengthy duration of this inquiry, and I continue to maintain those denials.

“I had been given a short opportunity to resign prior to termination, however I chose not to do that as it is tantamount to a concession of culpability, which I strenuously deny.”

Quaedvlieg alluded to the drawn-out and secretive nature of the investigation, and suggested he had been denied natural justice, saying he had “previously made a number of observations in relation to the inquiry processes”.

“I intend to pursue these more formally in the relevant forums. I will now take some time to fully consider my options.”

Malcolm Turnbull referred the case to Christian Porter, appointed attorney general in December, to prevent any apprehension of bias in the home affairs minister Peter Dutton deciding on Quaedvlieg’s fate.

Porter received two reports – one from the corruption watchdog and one from the the department of prime minister and cabinet – to consider before making a recommendation about the Border Force head.

In February the home affairs department head, Mike Pezzullo, told Senate estimates that Quaedvlieg is a statutory officer who can only be fired by the governor-general and confirmed he had earned about $500,000 while on leave, including superannuation.

Before the announcement on Thursday, Dutton responded to reports that Quaedvlieg’s dismissal was imminent by telling 2GB Radio it was “a sensitive time”.

“Obviously there’s been an investigation that’s taken place,” he said.

“The attorney general has been involved in the process and looked independently at all of the information available and there’s a conversation obviously that’s underway with Roman at the moment.”

Dutton said that he felt for Quaedvlieg, his girlfriend, his ex-wife and children.

“It’s not an easy situation and it’s not something that deserves to be across the front pages of the paper,” he said.

The Community and Public Sector Union national secretary, Nadine Flood, welcomed the decision on the basis the “zero tolerance approach to integrity issues” faced by ordinary staff should also apply at the top of Border Force.

“It’s been incredibly frustrating for staff to watch this drawn-out process in which a senior official was stood down and paid a very high salary for many months after highly questionable conduct,” she said.

Labor immigration spokesman, Shayne Neumann, criticised the “long, drawn-out, and expensive process” and called on the Turnbull government to restore stability to border force.

He said Labor was “extremely concerned” that details of the investigation had leaked to the media on multiple occasions.