It says that although the BBC had unlimited access to the Trust and its properties for two years, the films only explore the traditional aspects of its work, such as stately homes, and eschew some of the new projects that it believes sum up the new, modern character of the charity.
But Patrick Forbes, director and producer of the series, said the programmes accurately reflect the internal struggles that the Trust is experiencing as it tries to reconcile its established role as landowner and protector of stately homes with the desire to drive the charity into new territory.
"This is a real warts and all look at one of the country's most important organisations, and shows the real challenges of running such a huge and diverse organisation," he said.
But Jon Barton, director of communications at The National Trust, said: "There are exciting things happening for the Trust, but we feel that the BBC film crew went for the easier option of examining old and rather cliched stereotypes. Although we are disappointed about some aspects of the film we think they do show that the National Trust is going through a period of change and renewal, and the films really just provide an entertaining glimpse into some aspects of our work."
Forbes countered: "The National Trust has to recognise that its members don't join because it has a scheme of pilot projects, they join because they want to see old houses. The films highlight some of the tensions within the Trust and it would have been a crazy distortion not to reflect that."
The BBC 4 programmes, the first of which is screened this Sunday, highlight clashes between senior members over the acquisition of John Lennon's childhood home from his widow Yoko Ono.
Tim Knox, the Trust's head curator is filmed saying that he was "furious" with the Trust for investing in the house, and said that such moves were "publicity coups, not serious acquisitions".