But a Fair Work commissioner says the possibility of workers taking Melbourne Cup Day sickies might show why the department was proposing the measure.

The Fair Work Commission on Tuesday found against an instruction from the department allowing managers to request evidence from staff supporting reasons for unplanned absences, saying it was inconsistent with workplace terms set by the industrial umpire nearly three years ago.

Home Affairs in April published the instruction, which says that managers may request the documentary evidence in support of unplanned absences of fewer than three days.

"Managers may identify a pattern of absence over an extended period of time where an employee does not provide supporting documentation for absences less than three days on each occasion," the instruction said.

The main public sector union objected and started a dispute at the Fair Work Commission, arguing the instruction was inconsistent with the workplace determination setting industrial terms and conditions at the Home Affairs Department.

In a decision on Tuesday the industrial umpire found the department's instruction was inconsistent with the workplace terms, which said staff absent on personal leave for three or more consecutive days must provide satisfactory evidence for their reasons.

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Commissioner Leigh Johns said Melbourne Cup Day on Tuesday might demonstrate the reasons for the department's instructions.

"There are no doubt good management reasons for what is proposed in the procedural instruction," he said.

"As this decision is published on Melbourne Cup Day it might be envisaged that a number of workers were 'sick' yesterday (thus giving them a four-day long weekend), or may be 'sick' tomorrow celebrating the very elegant win by the winner of the Melbourne Cup. However, the workplace determination does not allow for requests for evidence of less than three days."

The Community and Public Sector Union argued that the workplace determination provided employees with an entitlement to take up to three days of leave without the requirement to produce documentary evidence.

However Home Affairs said there was no inconsistency between the instruction and the relevant part of the workplace determination, because there was simply no overlap between them.

Commissioner Johns said the department could advance an industrial claim regarding evidence for absences through enterprise bargaining.

The workplace determination, which Fair Work imposed after the department and staff could not reach an enterprise agreement in a long and bitter round of bargaining, has passed its nominal expiry date.

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