"Deploying the ship will free up commercial tankers to reconfigure and focus on moving aviation fuel," he said.
"This will help ease distribution issues in other regional centres."
Twelve army drivers will also be deployed to drive civilian tankers taking jet fuel to Auckland, Palmerston North and Napier around the clock from Thursday until Saturday, September 30.
The Endeavour, due to be decommissioned and replaced next year, has the ability to refuel ships at sea or in overseas ports from the 5500 tonnes of fuel in its four tanks.
It is the third New Zealand Navy oil tanker and supply vessel named Endeavour, after Captain James Cook's ship.
The Ruakaka Auckland Pipeline (RAP) has been out of order since last Thursday when an investigation in to a pressure drop revealed a serious leak only a couple of kilometres from the refinery.
A complex containment and recovery of spilled oil and contaminated ground water has been underway since then and the pipeline is being prepared for replacement of the damaged section.