"We've not met our high standards for operating small boats and that simply isn't good enough," said Captain Corina Bruce, commanding officer of HMNZS Philomel.
The inquiry found the incident was caused by several factors.
Apart from inadequate training of crew, it said HMNZS Philomel base standing orders for the conduct of coastal passages were out of date and led to no formal navigation plan or operational risk assessment for the voyage.
Prevailing wind and sea conditions also contributed to the VIP's grounding, the inquiry found.
Captain Bruce said the navy had moved swiftly to comply with recommendations and that he was confident the right training and procedures had been put in place to ensure such an incident was not repeated.
HMNZS Philomel standing orders have been updated to include a comprehensive direction on the use of the VIP barge and other navy small boats and tenders, Captain Bruce said.
A training regime has been implemented which ensures all small boat crews have the right skills to operate the installed navigational systems.
Training included the use of the Raymarine navigation system, GPS, radar and the echo sounder systems.
The Raymarine navigation system has been updated with the latest charts.
Neither alcohol nor fatigue were contributing factors.
The barge is now in operation after undertaking repair works.
Immediately after the grounding, Defence Minister Jonathan Coleman said he wanted some hard answers about the incident, which he described as an "embarrassment" for the navy.