The AFL club announced the deal on Wednesday, saying the partnership would help Fremantle remain in a strong position on and off the pitch.
But the agreement was met with opprobrium by critics, including ACT Senator David Pocock, who have accused Woodside of greenwashing their contribution to climate change.
"Fossil fuel companies, like Woodside and Santos, are expanding their operations, with no credible plans to decarbonise, while buying social licence by sponsoring sport," the former Wallaby wrote on X, formerly Twitter.
"The're betting on us not taking climate action, threatening the very sports they sponsor."
Mr Pocock penned an opinion piece for online media outlet WAtoday on Tuesday calling for sporting organisations to step up and play a part in addressing climate change.
Nobel Prize-winning climate scientist Bill Hare said he was disturbed to hear the club would not accept a science briefing from the Climate Council before signing the deal.
"Head in the sand is no way to fight global warning," he said in a tweet.
Last year, a group of 10 high-profile Dockers fans released an open letter encouraging the club to end its relationship with Woodside.
The group included Dr Hare, Fremantle's inaugural football manager Gerard McNeill, ex-player Dale Kickett, former WA premier Carmen Lawrence, author Tim Winton and former Woodside climate change advisor Alex Hillman.
"Climate change is already creating catastrophic and deadly conditions for communities here and overseas, alongside massive harm to natural systems that support our economy and wellbeing," the letter read.
"All responsible institutions have an obligation to signal that we must accelerate the transition to a decarbonised economy and cease all new fossil fuel projects."
Woodside has been a major sponsor of Fremantle since 2010 and the new deal will take their partnership to 15 years.
Woodside chief executive Meg O'Neill said the company was proud to work with Fremantle as it focused on "a lower carbon, equitable and sustainable energy future".
"As we move forward in the energy transition, partnerships with organisations such as the Dockers who prioritise sustainable outcomes will be critical," she said in a statement.
The Dockers said the renewed agreement reflects Woodside's commitment to have a positive impact on the club and the community.
"This includes the expansion of the Indigenous Program Partnership which encompasses the further development and implementation of Fremantle's next Stretch Reconciliation Action Plan," the club said.
Meanwhile, Woodside finds itself in a Federal Court dispute with traditional owners over its plan to begin seismic blasting off northern WA as part of its Scarborough Gas Project.
Traditional custodian Raelene Cooper argues Woodside did not properly consult her when seeking approval for the project.
Justice Craig Colvin has reserved his decision in the matter until Thursday.
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