Riven by internal feuding for decades, the NCPTA now faces criticism from the Charity Commission and demands for damages from the two trustees who complained about its management and financial controls.
Sandi Marshall, a former television journalist, and Sean Rogers, an education consultant, estimate they have spent thousands of pounds fighting their case.
Last year's legal bill for the NCPTA - which included the dispute with Ms Marshall and Mr Rogers - came to Pounds 6,185. The confederation claims much of the Charity Commission's report is untrue, but the organisation is no stranger to unrest.
In 1994 it paid out Pounds 10,000 after accusing Sheila Naybour, a former press officer, of being politically motivated. It had also tried to remove her from the trustee body and refused to accept her nomination for chair-elect.
During the past year, three committee members have resigned, two have retired, two were removed and Michael Pepper, the chief executive, walked out after only three months in post.
In its report, the commission accused trustees of spending Pounds 30,000 last year on meetings at a London hotel, with more than Pounds 40,000 being claimed on expenses. It said there was a lack of support for Mr Pepper, who was given no contract and whose job description was not finalised.
New trustees were often given a less than friendly welcome, and the charity's meetings, which often lasted eight hours, were described as confrontational. Annual meetings have been attracting fewer than 50 people.
Ian Price, a past chair who is now general secretary of the European Parents Association, was heavily criticised in the 36-page report.
But Mr Price, who is head of Wirral Hospital School, said he has not submitted any evidence to the commissioners or been given an individual interview.
Judith Wood, the present chair, said she had only one meeting on her own with the commission, which was conducted in front of staff in an open-plan office. She described the report as "subjective observations, mostly unsubstantiated, many contextually inaccurate, some totally factually incorrect", and said legal advice was being taken.
Both she and Mr Price disputed the cost of meetings, saying it came to Pounds 3,682 last year and not the Pounds 30,000 claimed by the commission.