Otago was carrying out sea trials off Melbourne to test her systems when the faults were found, the Defence Force said yesterday.
She had been due to arrive at Auckland's Devonport Naval Base on Friday.
The problem involved a manifold on one of the engines and it was expected to be fixed in time for sea trials tomorrow, Defence Minster Wayne Mapp said today.
"While it wasn't a major issue, it was disappointing," he said.
Commander Phil Bradshaw, director of the Defence communications group, said they were optimistic that the HMNZS Otago would be operational later today or early tomorrow and would leave for New Zealand later in the week.
More would be known about the ship's condition tomorrow and it would take four or five days to get to New Zealand, he said.
Otago is under warranty. The engine manufacturers MAN and the ship's builders BAE Systems are working with the ship's engineers to repair the faults.
The 1600 tonne, 85 metre-long ship is the first of the navy's two offshore patrol ships and its sister ship HMNZS Wellington, the final ship of seven in the Project Protector plan, is due to be delivered next month.
This is not the first time the navy has encountered difficulty with the shipment of new ships and the $500 million Project Protector programme has been bedevilled with problems and delays.
Dr Mapp said yesterday that delays and disputes were largely because the Labour government chose a one-off solution with the HMNZS Canterbury, which led to a very large repair bill.
Last month the Government said it had reached a $84.6m settlement with BAE Systems to fix problems with the Canterbury.
