A Perth court has heard the West Australian Government’s appeal against a Supreme Court decision overturning the environmental approval for its Roe 8 project.

The Save Beeliar Wetlands group successfully argued that the Environmental Protection Authority (EPA) ignored its own policies when it assessed the project last year.

The EPA was forced to argue that it did not have to follow its own guidleines.

Chief Justice Wayne Martin accepted the environmentalists’ point, and subsequently ruled the EPA's assessment and recommendations to the environment minister were invalid, as was the minister’s approval.

Roe 8 is part of the Barnett Government’s $1.6 billion Perth Freight Link project, which aims to connect Perth’s eastern industrial suburbs to Fremantle Port.

Thousands have rallied against the project, claiming it would destroy parts of the environmentally-significant Beeliar Wetlands.

The court was adjourned after two hours, but its decision will not be handed down for months.

“What we say is that the EPA never truly asked itself whether this proposal was environmentally acceptable or not,” Save the Beeliar Wetlands spokesperson Kate Kelly has told the ABC.

“I think that's because it had a fairly ... robust government looking to get that project fulfilled.”

Environment Minister Albert Jacob says he will not comment while the case is still in court.