The Wilderness Society had sought a judgement against then-state environment minister Bill Marmion for ruling that a gas hub at the site was environmentally acceptable, based on a recommendation from the state's Environmental Protection Agency.
The agency board was five members strong, however, four members of that board were forced to step aside from the decision-making portion of the assessment when it emerged they had conflicts of interest.
It was then left to EPA head Dr Paul Vogel to make the ultimate recommendation on the hub site, based on evidence gathered while the four members were still part of the investigation.
The EPA and Vogel had insisted that enough independence was brought to bear on the process for a substantial part of the decision-making process.
However, the Wilderness Society objected to this reasoning as part of a broader-ranging opposition to the hub.
It brought the case to the WA Supreme Court while the fate of the hub was still hanging in the balance but Woodside Petroleum has since abandoned a plan to locate an LNG hub at JPP.
In a decision handed down this morning, the chief justice found that the four members of the EPA who had stood aside had enough of an influence to call into question the ultimate decision.
"I have concluded that the purported decision of the EPA on 16 July 2012 to submit the assessment report to the minister was not a valid exercise of the powers conferred upon the EPA by the Act, because there had in fact been no valid assessment of the Browse LNG precinct proposal," the judgement reads.
"That is because the assessment was undertaken following a process which was directed and controlled by a number of decisions purportedly taken by the EPA but which were invalid because they were undertaken at meetings at which a number, often a majority and on one significant occasion all of those participating in the decision-making were disqualified from participation by reason of their pecuniary interest in the proposal."
The judgement is academic given Woodside has decided to walk away from the precinct but it is unclear whether the judgement will have an impact on a reported interest on behalf of the Department of State Development to use the JPP site as a supply hub for oil and gas operations in the region.
WA Environment Minister Albert Jacob issued a short statement: "The state government will carefully consider the Supreme Court's decision and will seek advice from the State Solicitor's Office before determining appropriate action."
