The Fair Work Commission handed down a draft determination for an enterprise agreement covering staff at the Department of Home Affairs on Friday afternoon, after five years of tense industrial negotiations, including strikes.

The 85-page agreement, and the accompanying 185-page decision, lay out the terms and conditions for workers at Home Affairs, including increasing the amount of work hours in a standard work day, explanations about how pay classifications will be unified and how much loading is paid for casual workers.

Staff at the department have already received a 4 per cent pay rise in June, when the commission released a part-determination. The second part of the pay rise, another 3 per cent, will be paid 12 months after the full determination is decided.

One of the major challenges in drafting the determination was dealing with the different pay rates and terms and conditions that applied to staff in the department, with some covered by the more generous agreement for customs and border protection workers and a different agreement for staff who had moved from what was then the department of immigration and citizenship.

Allowances made to staff was a major area of contention, with the decision by the full bench criticising both the unions and the department, saying the negotiation was a good opportunity for the department and "key protagonists" to rationalise the number of allowances to benefit both the department and employees.

"Unfortunately in our view the parties 'squibbed' it, though we acknowledge that the government’s Workplace Bargaining Policy provided no real incentive for a genuine conversation about rationalising allowances given the cap on salary increases," the full bench said.

"As a result, the commission is left with having to wade its way through what are at times diametrically opposed positions on a raft of allowances."

An allowance for staff working at airports will be phased out in the determination, reducing by 25 per cent every six months over a two-year period. More than a dozen other allowances will be scrapped by the determination.

Payment for acting at higher duties will only take place when those duties are worked for 10 days or more under the determination, but if an employee has already worked 10 days at a higher level in a calendar year, they will be paid more from the start of any further periods of acting at a higher level.

Both the union and the department will find wins and losses in the decision, with the full bench deciding in some cases to side with the department and other times with the union.

Home Affairs' wins include a decision to set the standard work day for all full time employees at seven hours and 30 minutes, up from the seven hours and 21 minutes requested by the union.

Casual staff will be paid a loading of 20 per cent on the standard hourly rate, below the 25 per cent the union said would be fair.

When rates of pay differed between agreements for public affairs and legal officers, the commission was more likely to go with the lower pay rates put forward by the department, but also identified many cases where the union and the department had the same starting point.

Handed down by the full bench of the commission, the determination is in draft form to allow the parties to identify any issues and work through them at a conference convened by the commission.

Both the Community and Public Sector Union and Home Affairs have criticised the other parties' conduct throughout the negotiations, the commission found neither party had acted in bad faith, but did concede boundaries were pushed.

"While the approaches adopted by the department and the CPSU in bargaining pushed the boundaries on occasions, the material before us does not support a finding that the conduct of the bargaining representatives was unreasonable during bargaining or that any of the bargaining representatives did not comply with the good faith bargaining requirements. Accordingly, these factors do not impact on the determination we make," the decision said.

A spokeswoman for the department said the determination and reasons for the decisions were welcomed by the department.

"The assessment period provided by the FWC to consider technical drafting issues, and preparatory work already undertaken by the department, will help ensure that the final workplace determination is implemented expeditiously," the spokeswoman said.

"The department will continue to comply fully with all directions issued by the FWC."

The 14,000 staff at Home Affairs have been told about the draft determination, with the department committing to keep them up to date.

"The department has already informed staff regarding the FWC’s draft determination; and will continue to communicate with staff and provide up-to-date information on this matter," the spokeswoman said.