"Significant petroleum infrastructure including the refinery at Marsden Pt, and the terminals at Tauranga and Napier are located on an east-facing coast so tsunami are a relevant threat," the report says.
A 2016 exercise assumed a 9.1 magnitude earthquake near the Kermadec Islands resulting in tsunami that hit most of the New Zealand coast.
"With events now expected to be larger there is greater risk that the refinery could be damaged, although the return periods are still considerable [i.e. rare]," the Hale and Twomey report says.
A 7.5m wave from a more localised event was assessed as having a 2500 year return period while a 4.8m wave had a return period of once every 500 years.
More distant events - such as an earthquake in South America generating tsunami - were considered more likely.
Refining New Zealand operates the country's only refinery and says it has tsunami event plans and for distant events would have more time to make the refinery safe and therefore easier to recover from any damage.
The location of the plant up the harbour also means it would not take a direct hit.
"A local/regional event is more difficult to manage and may result in the refinery being unavailable for a period of time."
With a higher tsunami risk and a higher major event risk from global data, the 0.25 to 0.33 chance of an event was now considered to be in 300 to 400 years, rather than one in every 400 to 500 years.
The refinery produces about 70 per cent of the country's petrol, 90 per cent of diesel, up to 85 per cent of bitumen and all jet fuel.
The Hale and Twomey report was completed at around the same time as the pipeline failure, cutting jet fuel supplies to Wiri in South Auckland for days and forcing airlines to put in place emergency refuel measures until supply was restored.
Damage to the pipeline is being blamed on a digger and in the report other threats to the 170km link include volcanic eruptions in Auckland.
The latest MBIE report on fuel system vulnerability had been due at the end of last year.
However, Energy and Resources Minister Megan Woods has ordered an inquiry into the failure of the pipeline with terms of reference to be determined early this year.
At the time of announcing the inquiry she said the September outage showed how vulnerable this key piece of infrastructure was.
Independent members will be appointed.
She said the inquiry would not only investigate the immediate causes of the outage but also the maintenance and operation practices at the pipeline and if they were fit for purpose.
"We will also look at how we can make our fuel supply more secure in the future – investigating options for improving resilience."