The internal ructions prompted the Auckland Council to cancel its $80,000 a year contract to manage the Te Puke O Tara Community Centre, a community focal point.
A legal challenge to the council's move failed last week in the High Court at Auckland.
Former centre manager Mary Gush, a member of the Otara Papatoetoe local board, said the dispute had not affected the fleamarket, and market proceeds would continue to fund community programmes.
Companies Office records show the society made $70,000 from fleamarket proceeds in 2008/09, when accounts were last lodged.
Mrs Gush said the community centre would remain an indoor venue for the Saturday market, even though the society has been asked to vacate.
"We've got 36 years of equipment sitting in the building, they have given us grace to get out," she said.
Her husband, Dennis Gush, is the Otara Labour co-chairman of the fleamarket committee.
This is far from the first brush with officialdom and political intrigue for the society, set up by Hillary College students and community leaders in the mid-70s as a grassroots response to community needs.
The pupils and community raised more than $250,000 to build the centre, and the Government and Manukau City Council contributed $90,000 each.
But the market's success led to a commercial and political backlash, and National MPs raised questions in Parliament about the market's legal standing and the use of market proceeds by the Labour Party.
The battle to keep the market going proved a springboard into politics for Auckland Mayor Len Brown.
The society failed to file returns from 2002-2007 and was struck off the incorporated societies register before being reinstated.
In 2009, the Manukau City Council terminated its lease over its failure to account for its spending and officials expressed concern that the centre was under-used.
In March, the Auckland Council community facilities department gained local board approval to cancel the society's contract.
A report by community facilities manager Brya Taylor noted concerns about the society's stability and ability to manage the centre and deliver services.
The report said that for much of its history, the society had operated under a lease which did not identify any specific activities and required only minimal reporting to the council.
Another local board member, Poutoa Papali'i, one of the society's founding members as a Hillary College pupil, returned last May as its chairman but resigned in September after planned changes to meet council contract requirements were rejected.
"There's no one else to blame - we did it to ourselves," Mr Papali'i said. "What's happened is devastating - it has taken a while to get over it. The society really have to look at themselves and take stock of what they've done."
But Mrs Gush said the society had a new board and would continue to provide community services.
