NSW Greens senator Lee Rhiannon has lost the top spot on the party's Senate ticket, meaning it is highly unlikely she will be returned to the Upper House at the next federal election.

Mehreen Faruqi, who is currently a NSW Upper House MLC, has won the preselection in a vote of NSW Greens members.

Sorry, this video has expired Mehreen Faruqi says she will campaign hard to win the Senate seat.

Senator Rhiannon's defeat comes after she was briefly excluded from the Greens party room earlier this year after a furious dispute with her colleagues.

"Some may see my loss as a success for those who denigrated myself and the political tradition of the Greens NSW," she told ABC News.

"Some members may see my defeat as a setback for a member-driven party and one committed to the radical transformative policies we need if we are to stop climate change and to create a more equal society.

"But I am confident that the Greens NSW will remain a member-driven party now we've had this preselection and Mehreen Faruqi is on her way way to the Senate."

She also said she had been "heartened" by the support she had received from younger members of the party who would represent it in the future.

Senator Rhiannon warmly congratulated Dr Faruqi and her preselection partners, Abigail Boyd and Rachael Jacob.

Faruqi wins vote by substantial margin

Dr Faruqi topped the count with 1,032 votes, followed by Senator Rhiannon on 742 votes, then Ms Boyd and Ms Jacobs.

Mehreen Faruqi has paid tribute to Senator Rhiannon's party work. ( Supplied )

Dr Faruqi has thanked Senator Rhiannon for her work.

"I feel really humbled that members have preselected me overwhelmingly to be their top candidate for the next federal election for the Senate. I can't thank members enough," she said.

"I have worked with Lee on so many fantastic issues for women's rights, green equality, for saving the greyhounds. So, I do thank her for that partnership and all that she has done for NSW, for Australia and for the Greens."

Federal party will be relieved, source says

One Greens source from New South Wales said the federal party would be relieved Senator Rhiannon would not be returning to the Federal Parliament after the next election.

"Lee was always keen to present this fight as a battle between grassroots members in New South Wales and a monolithic party machine," they said.

"Today's result proves that wasn't the real story."

Greens Senator for NSW, Lee Rhiannon, has conceded defeat although the vote has not been finalised. ( ABC News: Four Corners )

Senator Rhiannon had a dramatic falling out with her party in June and was temporarily suspended from voting in her partyroom.

She had adopted a different position on schools funding to leader Richard Di Natale and education spokeswoman Sarah Hanson-Young.

Other Greens senators accused her of breaking party rules and acting in bad faith when she campaigned against the Government's school funding legislation while they were still in negotiations over the bill with the Federal Government.

Senator Rhiannon argued she was just reflecting the views of local party members and lashed out at Greens who anonymously criticised her in the media, saying she felt "bullied and harassed".

The episode provoked a wider brawl between New South Wales Greens members and other branches.

Senator Rhiannon's term expires in 2019.