The hospital insists it's not a cost cutting measure, but that the payments are being made incorrectly.

It comes amid escalating budget pressures within Canberra's public health system, with the government handing over $60 million in extra funding to stave off service cuts.

Managers and nurses at Canberra Health Services were recently emailed saying the service wanted to crack down on how emergency duty was defined and interpreted.

The emergency duty recall entitles nurses to a minimum three-hour shift, to be paid overtime, plus a travel allowance.

Currently, many departments routinely offer emergency duty when there is a staff shortage and nurses are asked to work with less than 24 hours notice.

The hospital now only wants to pay the duty when there is an emergency that poses an immediate risk to health, life or property.

Internally, some nurses have questioned whether the changes are a cost-cutting measure, as the emergency duty is widely used as an incentive in many areas to fill urgent shift vacancies.

Some fear losing overtime payments they have come to rely on.

Currently, nurses are paid overtime when they accept an extra shift that pushes their fortnightly hours over 76.

It means many part time employees do not receive overtime payments for additional shifts (but are entitled to 25 per cent loading), unless they are called for an emergency duty shift.

The proposed changes would bring an end to those overtime payments.

While a spokeswoman for Canberra Health Services said it was not a cost cutting measure, an internal email sent by the executive director of nursing Denise Patterson said the change would ensure "we use our resources wisely and sustainably to reduce waste and improve efficiency".

The Australian Nurses And Midwifery Federation ACT branch secretary Matthew Daniel said poor management practices were to blame for the incorrect payment blunder.

He acknowledged some nurses could be worse off financially under the changes, and that there was some concern among nurses.

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But he said he supported the proposal because it would be the correct interpretation of the enterprise agreement.

"We all need to play by those rules - I cant justify those rules being interpreted as they have been," he said.

Mr Daniel said the payment had been widely used by some managers to fill shifts at short notice, instead of rostering properly.

"Trying to use the emergency recall as an incentive is a perverse incentive when really the problem is proper staffing in the first place," Mr Daniel said.

"There are instances where rosters for the coming month come out and they're not even filled to the minimum of the staffing that's required.

"They are now trying to undue the wrongs of the past and of course this is now causing the angst in how this should have been applied all along."

Mr Daniel said he hoped the part timers who had used the payments would not lose out, because they may instead be rostered for extra shifts on and given more certainty.

Opposition Health Spokeswoman Vicki Dunne said the move appeared to be an effective pay cut for hard working nurses.

"[Last week's] supplementary appropriation shows that the health budget is under serious stress," she said.

"I will pursue this matter during the inquiry into the supplementary appropriation in the coming weeks."

The health service spokeswoman said the proposal came about when it was found that the emergency duty clause in the nurses' enterprise agreement was being applied incorrectly

"Prior to making any changes, [Canberra Health Services] will enter a period of consultation with staff and relevant unions. This is regular practice where incorrect interpretations of industrial entitlements are identified," she said.