While the commission said the way in which some officers received the allowance and others did not had "serious inconsistencies", it ruled it was outside of its jurisdiction to change it.

The case between AFP police officers and the AFP was heard in the Fair Work Commission last week, and centres around irregularities between their current and former workplace agreements.

Under a previous workplace agreement, AFP officers used to get a deployment assistance allowance, worth as much as $5000 a year, if their first deployment was to Sydney headquarters, even if afterwards they went onto work at Sydney Airport.

But under the agreement, if an officer's first deployment was to Sydney Airport, this was not considered a "high cost area", making them ineligible for the payment.

In late 2011 when Sydney Airport became a first deployment for some, these officers missed out on the extra cash, despite the extra transport costs.

"Whether or not one classmate from the [AFP] College in a team receives $5000 a year more or less than another in the same team, arises solely from the coincidence of their first deployment between August and December 2011," the commission said in the ruling.

The new employment agreement, from 2012 to 2016, did not remedy the situation, according to the commission, saying only that the officers who used to get the allowance under the old agreement would continue to get it.

"Longer serving persons all consistently receive it, and shorter serving persons [deployed from the beginning of 2012] consistently do not," the judgement said.

The commission said this situation would change only if there was to be a review.

It agreed with the AFP police officers' arguments, saying they were "understandable and reasonable".

"This failure to pay the allowance for this small group has had a number of results, which together create this serious inconsistency," the commission said.

However, the AFP were successful in getting the case dismissed on jurisdictional grounds.

The commission said section 738-9 of the Fair Work Act meant that FWC can only deal with a dispute if the employer and employees have agreed in their enterprise agreement that FWC can deal with the matter, which was not the case.

The AFP's airport operations have a presence at airports in Adelaide, Brisbane, Cairns, Canberra, Darwin, Gold Coast, Melbourne, Perth and Sydney.

The AFP's presence at Sydney Airport has been boosted in the period since a March 2014 national audit office report criticised the AFP's resourcing strategy at the country's airports

"Although a number of factors are considered when determining the resourcing at each airport, the inherent risks presented by each airport, including passenger and aircraft movements and the level of criminality, are not explicitly taken into account.

"Some stakeholders would value a clearer articulation of the AFP's airport policing strategy," the audit said.

In October 2014, Justice Minister Michael Keenan announced an ­additional of 22 extra officers, taking the total number of armed federal police at Sydney airport to 118.