A union official slammed the move as a "bad sign" ahead of plans later this year to negotiate for a public service-wide workplace agreement.

Public Service Minister Katy Gallagher denied requests from both Australian Taxation Office commissioner Chris Jordan and the Australian Services Union's tax branch requesting workers be granted a 1 per cent pay rise for their "hard work and dedication".

The Albanese government will grant most public servants a 3 per cent pay increase in August this year as part of interim workplace arrangements for the public service while service-wide bargaining agreements are negotiated.

The move, announced in October last year, will override any expected pay increases as a part of existing agreements until August.

Mr Jordan sought an exception for his 20,000 staff, who he believed deserved pay boosts after a tough few years, asking for them to get an additional 1 per cent pay rise before then.

But the tax commissioner delivered the bad news to staff on Friday morning in an all-staff email.

"While the government acknowledged the important role we play and the individual commitment of employees across the ATO, I have been advised my request cannot be accommodated," Mr Jordan said.

In a separate letter to the Australian Services Union, Senator Gallagher explained that workforce pressures, including changes to pay conditions, experienced by the tax office were best resolved with collective bargaining.

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She explained it was a "complex task which will take time, commitment and support from agencies, employees and employee representatives".

"While I acknowledge the workforce pressures being experienced by the ATO and numerous other APS agencies, I do not consider the ATO's circumstances exceptional and as such, do not intend to make an exemption for the ATO at this time," she said in a letter on Wednesday.

"It is my view that these workforce pressures will be best remediated by restoring the ability of the APS to collectively bargain for improved terms and conditions, consistent with the government's broader reform plan."

The union's tax branch secretary Jeff Lapidos expressed his disappointment to tax office members shortly after Mr Jordan's email was sent.

He warned inflation far outstripped any of the promised pay increases by the Albanese government.

"It is cold comfort to be told we can look forward to a 3 per cent pay increase on 4 August 2023 when inflation is over 6 per cent and home loan interest rates continue to increase on top of that," Mr Lapidos said.

"The minister's refusal to approve our application is a bad sign for a good bargaining outcome. So we will have to consider how we can best use the new bargaining laws to get a good result for us."

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