The EDO represented a group of Tiwi islanders seeking to halt the pipeline project over concerns about its effect on a rainbow serpent named Ampiji and an underwater songline about a Crocodile Man.
Charlesworth said the EDO coinfected evidence and coached witnesses.
The judgement sparked opposition calls to withdraw public funding of the EDO,which receives about 10 per cent of its funding from state governments.
The WA government poured $150,000 into the EDO last financial year through Department of Biodiversity,Conservation and Attractions grants and has budgeted a further $75,000 annually over the next two years.
Charitable donations comprise about 75 per cent of the EDO’s funding.
Whitby scolded the EDO for its efforts in the Barossa claim but said it had an important role to play.
“I’m not very impressed ... I don’t think they should be very proud of that case and the way they conducted it,” he said.