They have been called in by Sean Rogers and Sandi Marshall, who have been suspended from its national executive.
Mr Rogers, who was due to take over as chair in May, and Ms Marshall, a trustee, claim the 40-year-old organisation is not fulfilling its objectives or giving value for money.
Just last month, auditors for the troubled organisation voiced concern at a further increase in the NCPTA's reserves, which now stand at more than Pounds 1 million.
King and Taylor, chartered accountants and registered auditors, also questioned its practice of sending out blank cheques.
A spokesman for the Charity Commissioners confirmed this week that they were investigating.
"We are looking into various concerns about the management of the NCPTA. We expect to have a meeting with the charity in the near future to gather further information which will help us to decide whether future action by us is required."
Ian Price, chairman, welcomed the investigation and said: "I know I personally have nothing to fear, and as I understand it neither does the organisation. When I was chair of finance, I carried out spot checks and never found any reason to be concerned, and I have no concerns as to the integrity, honesty and industriousness of any of the staff."
The NCPTA has been riven by battles between staff and trustees over who runs the organisation, founded to promote the relationship between parents and schools.
Last year Michael Pepper, a former Benefits Agency project leader who was appointed as its chief executive, left after just three months.
Six years ago Phil Woods, its general manager, was dismissed after a weekend meeting of the NCPTA's executive committee.
Mr Rogers and Ms Marshall, a Devon member, claim they were elected as trustees on a platform to reform the organisation.
They are alleged now to have brought the organisation into disrepute and were suspended in November after a five-hour meeting. They lost their appeal earlier this month.
Margaret Morrissey, press officer, and Judi Moylan, office administrator, had taken out grievance procedures against them and were refusing to work with Mr Rogers and Ms Marshall.
Mr Rogers is now considering legal action. Both he and Ms Marshall have called for a special general meeting of the NCPTA's membership. It is understood the legal bill for the NCPTA is already more than Pounds 5,000.
Mr Rogers is no stranger to dispute - he was once suspended as a Trafford councillor by the Labour party - but said: "I have never seen anything like this. I can take the rough and smooth in politics, but this is really something else."
Ms Marshall said: "The whole thing (the suspension hearing) was extremely distasteful. This is supposed to be a charity working for children and it doesn't give a stuff about children as far as I can see."