However, when one takes a step back, the rationality of the system begins to fall away. Others, including Informant editor Markus Mannheim, have made the point that granting clearances to an ever-increasing number of public servants and contractors leads to questionable security dividends in the first place. For starters, it means giving a greater number of people access to sensitive information.

But the biggest problem by far is the excessive waiting time that applicants for a clearance endure. I don't intend to criticise the Australian Government Security Vetting Agency; the problem lies with the overwhelming demand for clearances driven by organisational and cultural factors within the APS.

The consequences of these delays are far reaching. They actually create security risks because they lead to an increase in the number of temporary clearances being used, as well as a greater reliance on private companies to get through the never-ending vetting backlog. Questions have also been raised about whether a security clearance provides any guarantee that an individual will live up to their vetting.

I'll leave it to others to discuss those concerns. Instead, I'll focus on employment law. The security-vetting regime raises three issues pertinent to employment:

Let's start with recruitment. As I wrote earlier, a security clearance has almost become a prerequisite for APS employment. The problem here, as many people who have looked for work in the APS will be aware, is that, in order to apply for a clearance, an applicant must be sponsored by the employing agency.

Typically, unless a successful candidate already possesses the requisite clearance, agencies must be prepared for new employees to perform limited work (given they are yet to be vetted) for months, if not years in some cases, until the clearance comes through. It's little wonder that, as The Canberra Times has reported, some agencies, via their recruitment firms, began the (unlawful) practice of offering jobs only to candidates who already held clearances.

Yet it's usually employees who suffer the worst effects of these delays. Long waits for clearances can be demoralising and, in cases where the delay is particularly excessive, cause an employee to feel they are losing skills and experience. This doesn't even encompass the injury to new public servants, many of whom left another job to join the APS, who then find their clearance application is denied and their employment terminated. This can even happen years after engaging in any meaningful work.

Second: reviews for cause. Aside from regular security-clearance reviews, the vetting agency or the sponsoring agency may request that a "review for cause" be conducted. These allow for for circumstance where the agency has reason to believe a previously unknown security concern about a particular individual may exist.

However, there is scope to misuse the review for cause process, or, at the very least, for agencies to avoid certain obligations under the Public Service Act and enterprise agreements – for example, with respect to alleged misconduct. This was essentially the accusation brought against the Australian Signals Directorate in Applicant v Department of Defence (2014).

In that case, the signals directorate referred the applicant for a review for cause after issues with his workplace conduct were raised; conduct that the directorate argued amounted to a security concern. After the vetting agency carried out a review, the applicant's security clearance was withdrawn and the applicant's employment with the signals directorate was terminated on the basis that he no longer met an inherent requirement of the position: namely, holding the requisite clearance. The applicant then brought an unfair-dismissal claim in the Fair Work Commission against the Defence Department, alleging it had avoided following mandatory employee misconduct procedures.

Commissioner Barbara Deegan held that the applicant's dismissal was not unfair. She found there was no improper motive behind the directorate's referral of the applicant for a review for cause and that, in any event, the commission was not in a position to assess the correctness of the vetting agency's decision to withdraw the applicant's clearance.

In this way, the decision in Applicant takes us firmly into the territory of the third main employment-law problem with the vetting regime: termination of employment following the loss of a clearance.

The Applicant case illustrates a particular problem with security clearances and their interaction with industrial law rights under the Fair Work Act, the Public Service Act and other instruments. In essence, the security-vetting agency operates inside a black box, into which the Fair Work Commission and other tribunals won't tread.

While there are alternative ways to review adverse decisions of the vetting agency – including certain internal and external reviews to the Administration Appeals Tribunal or the APS merit protection commissioner (among others) – each of these carries its own impediments for the individual affected.

There is no easy solution to these problems, not least because there is no incentive for anyone to depart from current practice. There is no incentive for any manager to say a position does not require a security clearance, or to refrain from giving a document a classification that requires a clearance to access it, when the APS's dominant culture pulls in the other direction. Equally, there is no particular incentive for a vetting officer to approve a complex clearance application, even if they could potentially explain away or mitigate any concerns.

It's clear that changes must be made, but it's also clear they will need to come from the top.

John Wilson is the managing legal director of BAL Lawyers and an accredited specialist in industrial relations and employment law. He thanks his colleague Robert Allen for his help preparing this article.