Noongar activist Megan Krakouer has submitted a human rights complaint and accused the Greens of a "significant problem with racism" after a party staffer allegedly said "we don't want another Lidia Thorpe" during her preselection bid for this year's federal election.

Ms Krakouer's referee has made a complaint to the Greens following the process to her nomination for the federal seat of Fremantle.

"He asked how Megan would respond if she didn't agree with a Greens position on an issue and it could possibly impact on her integrity how would she react/respond," the referee's complaint stated, WA Today reports.

"...he went on to say 'we don't want another Lidia Thorpe.'"

Senator Thorpe resigned from the Greens over the Voice to Parliament, which she opposed. At the time, Greens federal leader Adam Bandt said the Victorian senator could remain in the party regardless of her position on the Voice.

After the referee stated they and Ms Krakouer are not related, the staffer allegedly followed-up asking if they were related in a "Blackfella way".

The Greens WA, Senator Thorpe and Ms Krakouer have been contacted for comment by National Indigenous Times.

On January 22, Ms Krakouer told her social media followers "I have now formally ended my membership with The Greens Party, effective this afternoon, and I feel a strong sense of liberation".

"At the appropriate time, I plan to reveal my experiences of racism, bias, power plays, no procedural fairness, discrimination, and unfair practices in The Greens that I endured at the hands of individuals who claim to be advocates for inclusivity," she wrote.

At the time, WA Greens co-convenor Giz Watson said Ms Krakouer had "very recently" joined the party, and "almost immediately nominated to be a candidate and was disappointed not to gain nomination for the (state) seat of Fremantle".

Ms Green said Greens WA followed usual pre-selection process.

Ms Krakouer told WA Today this week that the staffer's questions were offensive, inappropriate and assumed a "far-left alignment to my political views, which was not only an oversimplification but also mischaracterised my political stance".

She also said the process as a whole "was incredibly frustrating and, in my opinion, was deeply influenced by racism, discrimination, and prejudice".

In relation to the Senator Thorpe question, Ms Krakouer said "I am not Lidia Thorpe, and while I deeply respect her, my approach to politics is different."

"It reduced a well-respected and accomplished Indigenous leader to a negative stereotype, and made an unfair assumption about my own political approach," she told WA Today.

Ms Krakouer has reportedly submitted her own complaint to the Human Rights Commission in relation.

"In my opinion, the Greens have a significant problem with racism and a lack of respect for First Nations people," she told WA Today.

"It became apparent that I was being treated as a target rather than as an individual with my own unique contributions to offer.

"The entire process felt more like an orchestrated effort to suppress voices like mine rather than a fair and transparent assessment of candidates.

"There were repeated vexatious claims made against me, but despite these claims, there was no impartial or thorough investigation."

Her support from within the party is understood to have been mixed.

Last month Ms Krakouer joined Fatima Payman's Australia's Voice party in a bid for the Senate.

WA Greens director Dean Smith said questions to the referee were inappropriate and that the staffer had been spoken to.

A party spokesperson reportedly said: "The Greens WA followed our usual preselection process, which seeks to identify issues which may adversely impact the candidate and campaign, and reject the suggestion that doing so singles her out."

"While Ms Krakouer is now running for a rival party, we will respect her privacy by not discussing the reasons for that decision."