As tax office negotiators sit down with unions on Wednesday morning, the ATO boss has reached out directly to his agency's workers, to put the outline of a new approach on the table.

Mr Jordan will drop the demand for an extra 45 minutes work each week and make other key concessions, aimed at breaking the bargaining impasse that has gripped the agency for more than 18 months.

This morning's message is a dramatic departure from the provocative approach that saw the agency's senior executives given a 3 per cent pay rise on the day that the rank-and-file voted to reject the previous proposal.

The Commissioner told his workers by email this morning that he was committed to reaching an agreement with them and that some of the more controversial aspects fo the proposal that suffered a crushing no-vote by a margin of 85 per cent were to be dropped.

Gone is the demand to work an extra 45 minutes each week in return for an average pay rise of 2 per cent a year, the cutting of the $300 annual health and wellbeing allowance, the introduction of tougher rules around the taking of personal leave and several other contentious clauses.

"The new proposal reinstates the conditions that mattered most to you and keeps us at the forefront of APS pay and conditions," Mr Jordan said.

"This is a significant shift from the last offer and I hope it shows we have listened to you."

The Tax Office's shift of position came after the results of an all-staff survey into the reasons for December's no-vote were released.

Two-thirds of respondents were unhappy with the pay deal on offer and the request for a longer working day, nearly 40 per cent were worried about future rises in the cost of living and nearly one-third said they were concerned about the removal of the health and wellbeing allowance.

"Simply put, you felt the offer was not fair," a note sent to staff about the result read.

But Mr Jordan said on Wednesday that the improved performance of the agency had allowed the offer to be improved.

"The new proposal responds to your feedback and recognises the positive contribution and effort you've made to our business performance and Reinvention Program," Mr Jordan wrote.

"As Commissioner, I appreciate and have been delighted with our business results and positive changes to the client experience over the last 18 months; all achieved in a time when we were subject to numerous reviews and reductions in our staffing numbers."

But one workplace union indicated early that it was not impressed with the new deal with the Australian Services Union saying there were still important workplace rights being stripped away in the proposed EA.

"Commissioner Jordan has rolled over on some important issues, however he is still refusing to retain important rights at work," union official Jeff Lapidos said.

"The ASU needs these rights retained for a new enterprise agreement to be supported."