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"Clinical systems are back to normal with minimal disruption," medical director of patient services Richard Bunton said this afternoon.
"We want to thank patients for their understanding and a huge thank you to all our staff who have worked around this."
There were fears the computer system's collapse could affect elective surgery and other procedures at Dunedin Hospital.
However, Mr Bunton said today elective surgery was not affected by the IT failure.
"Elective surgery was not postponed at all over the two days," he said.
The failure of IT equipment meant file information could not be accessed, but that did not directly impede medical procedures including operations, he said.
The failure came after it was revealed last week that more than 3800 Southland Hospital mammograms were lost as a result of an IT failure.
Yesterday, Mr Bunton disputed a claim from Dunedin North MP and Labour associate health spokesman David Clark that the failure had put patient lives at risk and was a result of cost-cutting.
Dr Clark's claims were ''scare-mongering and scandalous'', he said.
''I am not minimising it. It is slowing things down, but it's not putting people at risk.''
Asked if the public could have confidence in the DHB's IT system given the latest failure and the earlier loss of mammograms, he said: ''I would think so.
"We do invest a lot in terms of having the appropriate equipment and it being upgraded. We believe it is [up to scratch], but I guess the public can't help but draw their own conclusions.''
IT workers ''right up to the top folk at IBM'' were working round the clock to get the system online.
Mr Bunton did not feel qualified to answer technical questions about why it might have failed. The server was ''rebooting'' and given its size this could take some time.
Dr Clark released a statement yesterday afternoon saying the collapse put patients' lives at risk and was symptomatic of cost-cutting across the health sector.
''Patient lives are at risk. Clinical leaders have been unable to access lab results, clinical notes, patient contact details, diaries and operating rosters, let alone communication tools like email.''
Health Minister Tony Ryall had placed ''so much pressure on DHBs that they are in survival mode''.