Chief operating officer Vivian Blake said there were "data integrity issues", with some reports produced through it considered unreliable.
Her report to the board's hospital advisory committee meeting this week indicated elective surgery was behind schedule by about a third.
But Mrs Blake said she could not put "hand on heart" and say this was the actual position.
It was expected the accuracy and volume of reporting would improve during the next two months.
The committee was told the new system - introduced in July with only three errors noted in 100,000 appointments transferred - was still subject to problems involving passwords and printers.
Regional chief information officer Grant Taylor said there were also problems with the layout and work flow of processes, which meant staff were now required to use a mouse rather than keyboards only.
Some board community-based services, including district nursing, reported complex data entry issues which were taking considerable time to resolve.
The committee was told the introduction of the system, including both the operational and capital costs, reached $3.959 million, which was $56,580 more than the amended budget for the project.
The original capital budget was $2.9 million.
Business analyst Grant Paris said the increased costs were operational and included overtime at the time of the changeover to the new system.
He said the salaried project team members worked hundreds of additional hours at no extra cost to the board, so were not included in his report.
Member Tahu Potiki said without the inclusion of those costs the report did not show the real cost of the project and it would be worthwhile recognising them.
Mr Paris said the board would also be spending an extra $12,000 in the next three months to fund a support person.
