In the midst of the Barnaby Joyce revelations last week, one of Canberra's highest profile public officials reached an inauspicious milestone.

Australian Border Force Commissioner Roman Quaedvlieg is believed to have now accrued more than $400,000 in salary payments while on leave, as an external investigation into his personal conduct drags on into a new year.

The case of the missing Commissioner who's still on a $619,905 remuneration package is shrouded in mystery, and has again put into sharp focus the standards applied to public officials as opposed to their political masters.

Under Senate estimates questioning last October, then-Immigration Department secretary Mike Pezzullo publicly confirmed the few facts that are known about the ABF's Commissioner's extended paid leave, which is now into at least its ninth month.

"The leave commenced in, I would have to refresh my memory, the latter part of May or possibly the early part of June," Mr Pezzullo told the 2017 parliamentary hearing.

Commissioner Quaedvlieg's alleged relationship with a member of the ABF is being examined by the Australian Commission for Law Enforcement Integrity, but this has never been officially acknowledged.

During the October Senate estimates hearing, Labor senator Kim Carr referred to the allegations while questioning the Departmental Secretary.

"The allegation is with regard to a relationship between staff members; is it not?" Senator Carr asked.

Mike Pezzullo at a Senate estimates committee. ( ABC News: Matt Roberts )

"I've seen press reporting to that effect," Mr Pezzullo replied during his estimates appearance.

"I'm not going to comment on that press reporting."

In fact, the new Home Affairs Department has been startlingly opaque about the whole issue, particularly considering the amount of public money being paid out to Commissioner Quaedvlieg during his extended absence.

The ABC has this week again asked the department fundamental questions of facts, such as how long the Commissioner has been on leave, what form of leave he's on, whether he continues to receive his full salary and what the status of the external investigation is.

The Department of Home Affairs is however refusing to clarify any aspect of the matter which has engulfed one of its most senior figures for more than eight months; a "no comment" to all questions has been its only response.

To date, Roman Quaedvlieg's only public comments on the matter have been through a statement to The Australian newspaper last year in which he insisted he had not acted inappropriately and expected to return to his post as ABF Commissioner.

The ABC understands Commissioner Quaedvlieg has confided to colleagues in Canberra that he's deeply frustrated by the duration of the investigation, which has recently edged towards a conclusion and is pending a final decision on any sanction he may face.

In an unexpected coincidence, that final decision now overlaps with the saga engulfing the Deputy Prime Minister — and comparisons between them are being made.

One source familiar with the Quaedvlieg case has described the political rallying around Barnaby Joyce by senior ministers as "hypocritically inconsistent" with the process the Commissioner has endured, saying "poetic licence" has been applied to interpreting the Ministerial Code to protect the Deputy Prime Minister, who is under scrutiny over his relationship with a former staff member.

In truth, the processes used to investigate and evaluate any wrongdoing in these cases are starkly different.

Canberra's bureaucracy, and indeed the military, is notoriously rules-based, with public servants and defence force personnel governed by strict codes of conduct, as well as clearly defined appeal rights through bodies such as the Administrative Appeals Tribunal.

Without specifically referring to Commissioner Quaedvlieg's situation, Mr Pezzullo made it clear in October that his workplace had a general policy applicable to everyone that all office relationships were to be declared "to ensure that there is no conflict of interest".

On the other hand, the rules governing personal relationships that often occur in the political offices inside Parliament House are far less clear. Much more latitude is given, and there is very little transparency.

In the wake of the Barnaby Joyce affair, thought has been given at senior levels within the Government to whether more rigorous standards could be applied in the ministerial code of conduct, so those involved in intimate relationships with a minister could be treated the same as a spouse or partner — that is, banned from employment in ministerial offices.

But where no crime or abuse of power is involved, a more comprehensive approach to rules covering parliamentary staff engaged in consensual relations would be difficult to design and enforce — especially when privacy and centuries-old protections of an MP's "privilege" are also factored in.