The ATO has told its 18,000 public servants the Coalition government's industrial relations policies are behind a wage offer of less than 1 per cent a year.

The ATO says the offer, of a 3 per cent up-front pay rise, followed by a 2 per cent increase 12 months later and a 1 per cent pay rise in its third year, maintains many of the conditions and entitlements that have been the key sticking points in the agency's marathon industrial dispute.

The main workplace union, the CPSU, acknowledged some improvement from the two offers comprehensively rejected by workers in December and May, but said it had "significant concerns" with the latest proposal.

The smaller Australian Services Union said the new offer was a renewed attack on workplace conditions at the agency, dressed up with 'weasel words'.

CPSU deputy secretary Melissa Donnelly claimed that "strong action" from union members at tax had brought "some improvement" after 1000 days of dispute, but said there remained serious problems with the latest offer.

"There are still significant concerns about the proposed deal, particularly the lack of real consultation processes and the employer's failure to address the extensive delays or deal with critical rostering issues affecting thousands of staff," Ms Donnelly said.

But the office's management says it has worked hard to develop an offer that puts back into the agreement key workplace rights and conditions that were stripped from previous rejected proposals.

Rank-and-file ATO public servants have not had a scheduled pay rise since June 2013 and the government's Abbott-era bargaining policy imposes a blanket-ban on back pay or sign-on bonuses.

So even if a new enterprise agreement could be agreed and implemented by the end of 2016, the latest pay offer amounts to less than 1 per cent a year over six-and-a-half years.

About 200 senior ATO executives scored a one-off 3 per cent pay rise in December, announced just hours after the majority of the workforce rejected the Tax Office's previous offer by an 85 per cent landslide.

A subsequent proposal was firmly rejected in May by an emphatic 71 per cent.

In her message sent out to all staff late on Wednesday, assistant commissioner of taxation Fiona Dillon referred twice to the constraints of the government's bargaining policy as the reason behind the ATO's inability to offer more money.

"We have listened to your feedback and have worked hard within the context of the Government's workplace bargaining policy to provide a new draft enterprise agreement," Ms Dillon wrote.

"The government's workplace bargaining policy allows a maximum pay increase of 6 per cent over three years, with no provision for back pay."

But Jeff Lapidos of the ASU told his members that the new proposal contained some "improvements" but it had many of the problems of the old proposals.

"It is staggering and very disappointing that the ASU has to again declare that commissioner [Chris] Jordan is misleading ATO employees when he says that his new proposal is maintaining our rights at work," Mr Lapidos wrote in his members' bulletin.