The company lodged a Section 18 notice with WA's Registrar of Aboriginal Sites on May 18 for permission to damage sites and indigenous groups have been given until next Friday to respond.
The issue threatens to further inflame relations between indigenous groups over the James Price Point development.
The Kimberley Land Council, which has negotiated a $1.5bn compensation package for the gas hub development, is understood to have helped Woodside draft its Section 18 application for ministerial consent to work in the area.
But the work program is bitterly opposed by the Goolarabooloo, who have been at odds with the KLC and who claim native title and cultural heritage rights over the area.
Goolarabooloo law boss Joseph Roe said Woodside's drilling program to test the feasibility of the James Price Point liquefied natural gas project would damage areas that had been recognised for their heritage values since 1991.
A Woodside spokesman said if approved, all activities in the area would be monitored by representatives of the traditional owners and be conducted under a cultural heritage management plan.
He said the company planned to undertake a limited range of engineering and environmental studies in areas south of James Price Point that are known to contain indigenous heritage sites. "In executing this work Woodside will avoid sites where possible, or minimise any disturbance to them," the spokesman said.
The drilling program is understood to include the area where pipes come ashore from the Browse Basin gas field and surrounding sand dunes, which contain extensive heritage areas.
"There are some old ceremonial grounds in there," Mr Roe said yesterday. "It is part of the song cycle and inside the song cycle there are old ceremonial grounds used for the initiation of boys."
Mr Roe said his family would contest the Section 18 application. "The whole family, including children, will go to the camp to stop the work," he said.
About 150 police reinforcements were sent to Broome last week to oversee the closure of one protest camp and ensure the company could get its earthmoving machinery to the James Price Point site.
A Goolarabooloo camp located closer to the worksite remains in place.
Mr Roe's lawyer, Andrew Chalk, said the matter was further complicated by the failure of the state government's compulsory acquisition of the James Price Point land, which he said threw the validity of the whole KLC agreement into question.
Mr Roe said Woodside's Section 18 application proved the company did not have all the approvals it needed to conduct its feasibility work, as it had claimed.
Mr Chalk has previously written to Woodside and its joint venture partners warning directors it would be a criminal offence to damage sites at James Price Point without approval under the Aboriginal Heritage Act. Mr Chalk has also provided Woodside with maps with the location of the sites.
He said Woodside's lack of approval called into question the WA government's decision last week to spend $1 million on police resources to help Woodside get its machinery past protesters.
Mr Chalk said it was possible Woodside might receive ministerial consent for its Section 18 application despite objections.
"The idea of the act affording protection is a bit of a mirage," he said.