Any damage to the sites integral to an important Aboriginal men's song cycle could leave the resources giant and its directors liable for criminal prosecution under the state's Aboriginal Heritage Act.
A government spokesman confirmed that the Barnett government succumbed to Woodside's wishes and withdrew the letters.
Andrew Chalk, lawyer for indigenous law boss Joseph Roe, who claims cultural responsibility for the area, said Woodside's actions had been "like asking a burglar not to tell a buyer that goods for sale are stolen".
Mr Chalk said letters from Woodside to the state government underscored how the government and the company had run roughshod over heritage concerns at the site near Broome in pursuit of development.
He said that the song cycle had been well documented for more than two decades but many details of it are considered men's business and must remain secret.
The WA Department of Indigenous Affairs wrote to Woodside after evaluating heritage claims following contentious site works in the middle of last year.
The visit followed the discovery of heritage records that pre-dated the Woodside proposal and included interviews with Mr Roe.
Lawyers claim information about the area's heritage value in the Kimberley Land Council's possession since 1991 was not included in the heritage advice given to Woodside more recently.
The material pre-dates Woodside's decision to investigate the gas hub site.
Scott Cane, an anthropologist commissioned by Indigenous Affairs, has confirmed Mr Roe's standing as a significant figure in indigenous law for the area.
"It is clear to me that his knowledge of the religious tradition is comprehensive and his commitment to that 'law' is consistent with both his knowledge of the tradition and his ancestral responsibility to it," Dr Cane wrote in his report on July 16.
Dr Cane's report follows the rejection of DIA's advice about the significance of the area the previous year.
In a letter to the state government dated September 5, 2011, Woodside thanked the department for withdrawing an earlier letter expressing the potential significance of the area. It asked that further advice from the department in relation to a "possible site" in the vicinity of the proposed gas hub also be withdrawn.
Woodside had said the area involved was too big and the timing was vexatious.
The company objected to details of the significance of the area being withheld on the basis they were for initiated males.
Woodside said it was being denied "procedural fairness".
A spokesman for WA Education, Energy and Indigenous Affairs Minister Peter Collier confirmed the advice to Woodside had been withdrawn. "The department withdrew the letter and maps as the content was, upon review, unhelpful and did not properly advise Woodside of known registered sites," he said.
A Woodside spokeswoman declined to comment specifically on communications with the state government.
But in a statement, Woodside said the company was working closely with senior traditional owners to identify and carefully manage Aboriginal cultural heritage at the site of the proposed gas hub. "We conduct our activities under the supervision of traditional owner monitors," it said.
"Comprehensive ethnographic and archeological surveys conducted by traditional owners have been completed to identify the location and nature of Aboriginal heritage sites."
Woodside would seek all additional consents and approvals needed to conduct any activities in areas known to contain Aboriginal heritage.
The project, with a $1.3bn social benefit package for Kimberley Aborigines, has split Broome's indigenous community and drawn environmental protesters from all over Australia.