Michael Pepper's hasty departure last week after just three months in the post of chief executive is symptomatic of the organisation's division and turmoil. There are battles between staff and trustees, sniping and backbiting among prominent members, and splits between chairmen, resulting in a breakaway group being set up last year.
Anonymous faxes alleging everything from drunkenness among the parents' leaders to financial mismanagement have been arriving at newspaper offices.
Although the national charity has more than Pounds 1 million in the bank, it has been turning down applications from local federations for money to spend on photocopying and fax machines.
Mr Pepper is believed to have negotiated a salary of Pounds 38,000 - Pounds 3,000 more than his job will now be advertised at - and to have received removal expenses of nearly Pounds 7,000.
Last year, the NCPTA paid out nearly Pounds 106,000 in wages to its five full-time and three part-time staff and another Pounds 10,500 in expenses for them.
Committee meetings, held in London every six to eight weeks, cost more than Pounds 29,000, and a further Pounds 50,000 went on office expenses. In the run-up to its annual conference this year, trustees voiced concerns about the amount of money held in reserve and the quality of the service provided by the charity to its 12,000 member schools. And this week, grass-roots members were asking what their annual subscriptions of up to Pounds 80 were actually being spent on and what was going on.
"We are a registered charity and have gone to all this effort to recruit a chief executive and, after a few months, the man has quit - something is not right here," said the chairman of one federation. "I don't know whether it is the organisation or him. It might be for personal reasons but it leaves you wondering and suspicious."
Mr Pepper, a former benefits agency project leader, had been brought in to make the management of the NCPTA more professional. His departure last week was the second swift exit from the charity. Six years ago, Phil Woods was dismissed as its general manager after a weekend meeting of the confederation's executive.
Sean Rogers, chair-elect, said that Mr Pepper's departure was unfortunate. "The principle of a chief executive for the NCPTA is still right. This was just a case of wrong man, right job."
Tensions have simmered for years over who actually runs the organisation - the staff or the 15 trustees who set policy. Before this year's annual conference, there were complaints that both sides were using the internal memo process to wage personal attacks.
The NCPTA was founded to promote the relationship between parents and schools.
A key problem for the organisation has been how to reconcile its charitable status with a crusading role, without facing claims that it has become political.
The divisions and internecine warfare that have dogged it over the past decade have been party political and personal.
They came to a head in 1992 when Peter Rippon, the then chair-elect, along with 14 of the NCPTA's most active area federations issued a separate, more critical response to the then education secretary John Patten's controversial Choice and Diversity White Paper.
He was supported by four members of the executive committee and four vice-presidents as well as former membership secretary Elaine Whalley, and former press officer Sheila Naybour.
The official version was put together by press officer and former chairwoman Margaret Morrissey.
Mrs Morrissey, who is a former Conservative activist, is the public face of the NCPTA, regularly talking to the press, appearing on TV and radio and having meetings with ministers. Others in the organisation undoubtedly feel that different voices should be heard.
"The important thing as far as I am concerned is that we get the message over," she said. "Quite frankly, how it's done and who does it is not the issue. "
In 1993, Ms Naybour unsuccessfully tried to get the Charity Commission to conduct a root and branch audit.
She believes now that the internal rows have made the NCPTA unmanageable and said: "There is a cancer at the heart of the organisation."
The bulk of schools that affiliate to the NCPTA do so for the insurance cover it offers for events such as fetes. The NCPTA also provides leaflets, giving advice such as food regulations for cake stalls, how to protect children from skin cancer and insurance for fund-raising bungee jumps.
Up to 1986, the NCPTA was dominated by teachers but, in 1987, its constitution changed to give parents a two-thirds majority on its executive committee.
This year, there are eight parent trustees and four teacher trustees but its chairman is Ian Price, the head of a special school. He said: "We can't pretend there are not tensions in our organisation, and we must continue to go forward to remove the inherent cancer from the NCPTA so that it can assume its rightful place as a potent, national parents' body."
Last year, former chairman Larry Goodband set up the rival Alliance of Parents and Schools.