The Public Service Association (PSA) said the new system — which took up to four times longer to use — was causing staff burnout and was a risk to patient wellbeing.
Health New Zealand Te Whatu Ora (HNZ) acknowledged the switch to the new system had "not gone as smoothly as planned" but did not comment on whether it would take on more staff to tackle delays and prevent burnout.
The patient management system, South Island Patient Information Care System (SIPICS), was introduced in the hospital last November.
Staff last week described the change as a disaster, highlighting ongoing issues with wrong or missing patient information and processing delays, as reported by the Otago Daily Times.
A PSA delegate, who did not wish to be named, said the rollout had been "really messy" and a lot of union members had raised concerns with the PSA.
Everything from booking appointments to updating patient details was taking three or four times longer than it used to. So much more time was needed to complete tasks compared with the old system.
"It's been a really stressful, frustrating and hard time.
"A lot of us, a lot of people are very exhausted and burnt out, and it just doesn't feel like it's going to get better any time soon."
Delegates had been raising concerns via numerous different channels since the beginning, including via a letter last month and in a meeting with the SIPICS project team earlier this month.
"In that meeting, it was acknowledged that work needed to be done to fix various issues ... but there's no clear indication of how long it's going to take, which for us is just really frustrating.
"There's a lot of concern that there's just not enough staff resources for how much extra work we actually have to do."
A further issue was the potential for burned out staff to make mistakes.
"We're really concerned about the safety of our patients as well."
The delegate called for more help, more staff, and better communication.
Staff were asking about the system, but were disheartened by how little they had received in the way of answers.
"It's people, it's healthcare, it's important."
PSA organiser Poppy Stowell said SIPICS had some merits over the old system, but changes needed the required infrastructure and staffing to be effective.
Members had reported increasing workloads for some time.
"While Te Whatu Ora Southern has indicated it would approve extra short-term support for certain administrative areas, we are unaware of members successfully accessing this.
"It also seems that meaningful permanent staff increases are off the table, despite members highlighting that this will be needed even if the system is fully functional."
Staff in the health system were already stretched thin enough, and the PSA welcomed working with the employer to find a meaningful solution, she said.
HNZ data and digital chief Leigh Donoghue thanked hospital staff for their efforts in a challenging time.
SIPICS connected Southern with the rest of the South Island for improved continuity of care, he said.
The system was already in use in Nelson, Marlborough, Canterbury and South Canterbury.
While a period of adjustment was always to be expected in changing to a new IT system, the transfer to SIPICS had been "particularly challenging".
This was partly due to older infrastructure that HNZ was in the process of updating, as well as issues moving data from the old system.
"This has not gone as smoothly as planned.
"There are known issues which are being addressed by our IT support team with fixes applied along with appropriate data validation."
The team was working with all Southern staff to resolve issues and patient safety remained a priority.
HNZ Southern did not answer questions about the possibility of a staffing boost by ODT deadline yesterday.
