Commonwealth-owned corporation Airservices Australia told employees to use their recreation leave during the public service's quiet period, a time when government agencies are traditionally emptied of staff.

Justice Debra Mortimer said the employer had breached its workplace agreement with staff, which required bosses to consult each employee on their leave periods.

The court on Friday found Airservices Australia forced two staff members to take their recreation leave during the 2015-16 shutdown despite a warning the corporation's decision could contradict their enterprise agreement.

Airservices Australia, which provides aviation safety services around the nation, told staff members in October 2015 when they would take leave over the shutdown.

It forced simulator support officer Tristan Bell to take six days of leave, as there were no bookings for him to provide training in that period.

The employer also required airways data technician Orazio Lo Castro to take two days of leave.

Both employees had planned to use the leave otherwise.

Justice Mortimer said a letter on December 18, 2015 from the Civil Air Operations Officers' Association representing staff warned Airservices bosses they may have contravened the workplace deal.

The employer nonetheless went ahead and forced its employees to take their leave, Justice Mortimer said.

A training manager replied to the letter in January 2016, arguing Airservices' shutdown period applied to all "non-operational staff", and that the corporation required them to use a combination of leave and public holiday stand-down.

Justice Mortimer said evidence showed the corporation only addressed the union's complaint after it was too late to do anything about it for the two staff members.

She said the leave periods were small, but added that "each and every period of leave is important to an employee, who has a fixed amount of leave".

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Staff working regular shifts five days a week received four weeks of recreation leave a year under the enterprise agreement, which says employers must consult staff when allocating leave.

Justice Mortimer said Airservices Australia failed to consult staff, and told it to pay the penalty to the union.

In deciding the fine, she took into account the corporation's decision to credit staff employed at the time with five days' recreation leave.

The lack of simulator training work during the shutdown period was "beside the point" in light of the workplace agreement, she said.

"The point of consultation is that there may have been other factors, relevant to those employees, which may have persuaded the respondent it should not require these two employees to take leave, despite the absence of simulator work," Justice Mortimer said.

Airservices Australia was legally obliged to consult staff on their leave and could not decide to opt out, she said.

There was no evidence it sought legal advice when receiving the union's letter about consulting staff on recreation leave in December 2015, Justice Mortimer said.