Among concerns are the length of emergency department stays, radiology waiting times and poor data on numbers waiting, and access to colonoscopies.
Although the national body has input into service improvement around the country, it is the first time any hospital has had such a comprehensive review.
Those involved with the assessment announced yesterday are keen to see it portrayed as a positive move, rather than an indictment of the district health board.
National Health Board service improvement manager Jill Lane said both the district health board and the national body had come to the agreement that it was a good idea to jointly review the systems.
It was a matter of making sure things were as good as they could be and supporting the board to make any improvements needed.
The assessment was not about individual clinical practice, but would look at patient flow and administrative systems within the hospital.
Ms Lane, who will lead the team, said it would have its report completed by the end of June.
She was not anticipating a "great big doorstop of a report", but one with practical operational recommendations.
Others on the team will be Ministry of Health chief nurse Jane O'Malley, Canterbury District Health Board emergency specialist Prof Mike Ardagh and another senior medical specialist, yet to be named.
As well as the concerns mentioned earlier, the National Health Board also cited comments by the expert panel on neurosurgery about the lack of spending on neurosurgery facilities and its effect on the viability of the service.
Booking processes out of step with national practice, such as those for cardiac surgery, will also be looked at.
If any other service issues become apparent during the assessment, they will also be investigated, along with barriers to effective risk management and service improvement.
Ms Lane, whose background is in nursing and who was chief operating officer at Hutt Valley District Health Board, said her discussions with clinical and management staff so far had been very constructive.
Association of Salaried Medical Specialists executive director Ian Powell agreed the move was unusual.
He said it was timely and should not be seen as threatening to health professionals.
He had some concern about the tightness of the time allowed for the report, but the national board would not be "coming cold" to the task, as it had already held discussions with staff.
Chief operating officer (Otago) Vivian Blake said the assessment was not a "witch hunt" and she did not think staff would be threatened by it.
Board chief executive Brian Rousseau is on leave and not available for comment, but he had agreed to the assessment process before he left.
Long-standing concerns
• Long stays in emergency department.
• Long radiology waiting lists.
• Booking processes inconsistent with national practice.
• Access to colonoscopies.
• Level of investment in neurosurgery.
