The refinery remained on track for conversion to take place in the first half of next year, she said.
But the association said the refinery's closure would increase the barrier to easy achievement of low emissions transport.
"To maximise the future opportunities, and reduce potential cost barriers, and ensure that the required equipment at the refinery is maintained in a suitable form, the objective should be to provide incentives for Refining NZ to keep assets that may be used for refining of alternative fuels," executive officer Brian Cox said.
He said a biorefinery could produce biofuels for heavy transport, marine - such as the Inter-islander - rail and sustainable aviation fuel.
"Use of the existing site will be very important if domestic biofuels are to be available sooner, with the consequential greenhouse gas emissions reduction. Obtaining resource consents to build new green-field biorefineries and further development of the production capability can be expected to take up to 10 years."
Cox said the maximum value of the refinery for future biofuels production would be achieved if the Government assisted Refining NZ to keep the facility operational, at least for a period in which to develop a future plan for repurposing the assets.
The refinery spokeswoman said Marsden Pt has huge potential being a large industrial consented site, with deep water port access, large electricity and gas connections and a very capable workforce.
"We want to explore what the best opportunities are for the site as we move forward, whether it's the import or export of energy, its production or storage. And whatever form that fuel or energy might be in the future from biofuels, sustainable aviation fuel, hydrogen, LNG and electricity. At this point we are focused on identifying all of the opportunities."