The full bench of the commission handed down a draft determination on Friday, ruling on every clause of the agreement covering employees at the Department of Home Affairs after the government and unions failed to come to an agreement after years of negotiations.

Introduced by former Public Service Commissioner John Lloyd, the controversial workplace bargaining policy restricted agencies from offering more than 2 per cent annual pay increases and blocked conditions from being improved unless traded with other conditions or allowances.

Before the creation of Home Affairs as a mega-department, employees were covered by the agreement for the former department of immigration and citizenship, and others by that which covered former customs and border protection staff with markedly different conditions.

Finding a single set of terms and conditions after the machinery of government change that brought immigration and customs workers together "in a way that balanced the interests of the department and its employees was made nigh on impossible by the absence in the government’s workplace bargaining policy of any meaningful scope to recognise the unique circumstances existing in this case," the Fair Work decision said.

The 185-page decision not only laid out how pay increases should be calculated and the allowances to stay or be scrapped, but also made comments on the conduct of the parties involved and the quality of the evidence given.

The policies and actions of the Australian Public Service Commission also came in for a serve, even though the commission wasn't actually a party to the case.

"We ... suggest that consideration be given incorporating some flexibility into the government’s workplace bargaining policy to deal with the difficulties which frequently arise in bargaining where machinery of government changes are involved," the decision said.

While the interactions between the department and the commission were "overwhelmingly ... consistent with the APSC's role" under the government bargaining policy, Fair Work did take issue with conduct of the commission during negotiations.

"We also consider that there was at least one instance where in our view the APSC inappropriately exceeded its 'gatekeeper' role", the decision said.

That instance was a series of emails between the commission and officials at the department, sent in July 2015 that showed the APSC had sought ministerial approval of an agreement to be voted on by employees in order for it to be part of a "coordinated ballot timing strategy" with other agencies' agreements.

In an email from the commission to some agencies, a commission staff member said "we think there is value in a coordinated approach to timing, such that a number of EAs are put out to a vote on or near the same day".

Home Affairs staff voted down an agreement for the second time in September of that year.

"The above email extracts show the APSC engaging in a strategic role regarding the timing of votes on proposed agency agreements," the full bench said.

"This in our view is inconsistent with the role of the APSC as set out in administering the government’s workplace bargaining policy and providing advice to agency on the government’s employment and workplace relations policies."

The Public Service Commission has responded to the assessment made in the decision, saying "The content of the governments’ workplace bargaining policy is a matter for government to decide".

"Machinery of government changes are not uncommon and agencies affected continue to negotiate new enterprise agreements," a spokeswoman said.

On the instance where the commission was said to have exceeded its role, the commission only said "The role of the APSC is to provide support and advice to agencies on the government’s employment and workplace policies".

The Community and Public Sector Union has long railed against the role played by the Public Service Commission and the government's bargaining policy, labelling it as the reason the negotiations took years.

"The Government’s harsh and unreasonable public sector bargaining policy drove much of the agenda that’s behind this ugly dispute, as Fair Work itself has recognised in criticising the conduct of the Australian Public Service Commission," national secretary Nadine Flood said.

"It took more than four years to settle bargaining for the vast majority of Commonwealth workers and yet Home Affairs was the only department that was even able to access arbitration through Fair Work after the Commonwealth applied to terminate industrial action at international airports."

A Home Affairs spokesman said "the department sought Fair Work Commission intervention to suspend the protected industrial action in the department so we could return to bargaining".

"The CPSU instead submitted that the Fair Work Commission should terminate the protected industrial action, effectively terminating any possibility of further bargaining and initiating arbitration on October 5, 2016," the spokesman said.