A Federal Court judge has found the board of the South West Aboriginal Medical Service used factional control and "oppressive conduct" to avoid scrutiny and unfairly expel members and a director.

The ruling, reported by the ABC, follows 12 months of turmoil within SWAMS, a not-for-profit with about 1,200 members across Noongar country in south west Western Australia.

In June, SWAMS members marched on its headquarters in Bunbury to demand the dissolution of its board amidst ongoing turmoil in the organisation. Police were called to the headquarters after members staged a protest and held a meeting in the building's lobby, calling for the deposal of chair Phillip Ugle and former chair-turned-director, Ernie Hill.

SWAMS' subsequent decision to expel 20 members, including director Lesley Ugle, sparked legal action.

In his judgement Justice Craig Colvin said Mr Phillip Ugle and Mr Hill used factional control over the board of directors to maintain their control over SWAMS' affairs and avoid scrutiny of members and other directors, the ABC reports.

Mr Ugle told the ABC he acknowledged the court's decision and was carefully reviewing the judgement and obtaining legal advice. He said he remained committed to the medical service and its core purpose, and had not ruled out an appeal against the ruling.

"I do not intend to step down as chair," he said.

"I believe accountability rests with the membership, and I will stand before them and allow them to make an informed decision regarding my position."