A decision was handed down by the Fair Work Commission on Wednesday backing the main public sector union in its lengthy battle against the department over three new policies introduced between September 2020 and February this year.

One update to the department's dress standards policy ruled sleeveless tops, dresses and blouses were "unsuitable" for the workplace and extended the rule to those working from home.

The commission ruled in favour of the Community and Public Sector Union and its members, arguing the department had been "short-sighted".

Department heads will now need to consult with staff and the union on the policies.

"It is important that employees be consulted about policies that may impact upon them," the Fair Work Commission's decision read.

"It is short-sighted of the department to not recognise the benefit of consulting with its employees about policies that affect employees and the recognised benefits of co-designing workplace policies.

"That is a matter that [the Home Affairs Department] must live with."

Under an earlier workplace agreement, which came into effect in 2019, the department was required to give its employees a minimum of two weeks to comment on new policies, procedures and guidelines or proposed changes to existing ones.

The department argued to the commission there were "practical difficulties" involved in speaking to staff and the union each time they planned to introduce or change a policy.

The two policies introduced in September 2020 related to employee use of social media and updates to dealing with vulnerable children.

A third policy, introduced in February months after the union initiated talks with Home Affairs, updated the department's dress and appearance standards, requiring staff to undertake additional hygiene requirements and maintain a "neat and tidy appearance".

It also excluded staff from wearing sleeveless tops, dresses and blouses, considered unsuitable attire, in both the office and while working from home.

The union's deputy national president, Brooke Muscat, welcomed the commission's decision, adding consultation was important to ensure staff understood policy changes.

"Our members are disappointed and frustrated that it has taken almost a year of trying to talk sense to the department," Ms Muscat said.

"Policies such as dealing with vulnerable children should absolutely be a matter of consultation - it will only strengthen the final product based on the wealth of practical experience our members have.

"We hope that this decision will lead to Home Affairs acting like a reasonable employer."

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An agreement was reached in February 2019 between the union and Home Affairs following a full bench ruling by the Fair Work Commission forcing the department to consult with employees prior to changes made.

The commission's ruling came weeks after an employee census revealed staff morale in the department was lower than other comparable agencies and departments.

Home Affairs' 2020 census results showed it had below-average ratings from employees on the quality of workplace culture, staff inclusion, and workplace conditions.

Only around half of those surveyed at Home Affairs said they would recommend the department as a good place to work.

The department was asked for comment regarding the Fair Work Commission's ruling but it did not respond in time for publication.