The nurses and their union claim the government failed to deliver an across-the-board lift in night penalty rates accepted in negotiations for their latest industrial agreement, leaving some nightshift workers being paid less than their colleagues for identical work.

Health Minister Simon Corbell has rejected the claim, saying the issue was not raised in negotiations and the Fair Work Commission had confirmed the agreement's terms were clear.

Australian Nursing and Midwifery Federation ACT secretary Jenny Miragaya said the federation had made an error in leaving the four-year agreement with terms for a 22.5 per cent penalty rate payment for 12-hour night shift workers, when other night shift workers were bumped up to 25 per cent, but the government was also implicated.

"When we raised it verbally with ACT Health officials in early 2014 it was agreed it was an oversight," she said.

"It just is fundamentally unfair getting paid a lesser penalty."

Three nurses who had worked 12-hour night shifts at the hospital said the latest agreement had been "sold" to them as providing 25 per cent night rates, and claimed the failure to change was part of a government attempt to move away from 12-hour rostering.

"It galls me because they're so pig-headed, because it's not saving them much, and it's their way of trying to get them off the 12-hour shifts," one nurse said.

The nurses receive about $1 per hour less than night shift nurses who worked shifts of eight or 10 hours. Ms Miragaya said the result was an annual loss of about $1300 for the lowest level enrolled nurses to about $2200 for highest-grade registered nurses permanently working the longest shifts.

There are 11 nursing staff regularly working 12 hour night shifts, mainly in the Neonatal Unit and after hours manager roles, while another 10 staff members had also worked a 12-hour shift in the last fortnight, the minister said.

Mr Corbell said the entire current agreement – approved by the Fair Work Commission in March 2014, backdated to that January and in effect until 2017 – was endorsed by the federation and voted for by its members. The commission confirmed there was no ambiguity when the issue was raised in dispute resolution in May this year.

"If it had ruled differently the government would have been happy to revisit that part of the enterprise agreement," he said.

"It is not appropriate for governments to renegotiate enterprise agreements after they have been voted on and enacted just because one party decides in hindsight they would have liked a different outcome."

The minister, who is not contesting the 2016 election, said the government was happy to address this issue during the negotiations for the next agreement.

"The ACT's night penalty rates for nurses are, regardless of the two different rates, still amongst the highest in Australia."

The three nurses said the 12-hour shifts, which are voluntary, provided the best work-life balance for many staff. Mr Corbell said the pay issue was not related to the government's preferred option for 10-hour shifts.