Many more are expected to follow in protest at the deal with the supermarket chain which they claim contravenes World Health Authority guidelines on the independence of health workers and the charity's own principles.
An extraordinary general meeting of the trust, which promotes breast- feeding and natural childbirth, was called by rebel members unhappy that trustees had taken the supermarket's money without consulting the 55,000 members.
The decision followed a move to raise subscription levels which had also upset supporters who feared the higher rate would confirm the charity's image as a white middle-class organisation.
At an emotional meeting in Acton town hall, west London, dozens of counsellors and ordinary members accused trustees of a lack of democracy and of abandoning what the trust had always stood for.
Sainsbury's is the only leading supermarket chain to produce an own-brand formula, and the rebels claims that accepting sponsorship could be viewed as endorsing that brand. But despite significant support in the hall, the rebels failed to win over more than 3,000 members who had already voted by post.
Leah Granat, a counsellor from Glasgow who also tutors other counsellors, said she had been offering independent information to mothers for 10 years. "Accepting money from a formula milk manufacturer totally compromises that position. It's very sad," she said.
Sheila Perkins, who resigned as chair of the trust's breast-feeding promotion group when the sponsorship was first revealed last November, announced she was resigning as a member, counsellor and tutor altogether. "Information has been suppressed," she said.
Caroline King, a member who had called for all subscription fees to be approved by members, said there were concerns about the way the voting had been run. The council of trustees had sent four pages opposing the rebels' resolutions with the voting forms. But the rebels, who paid for their own campaign, had not even been permitted to have a membership list of people to contact. However, she said the trustees had now heard the strength of feeling. "It's over to them to demonstrate by their actions the future of the National Childbirth Trust."
Ruth Stone, the trust's chair, said she regretted the resignations, but believed the NCT would be stronger as a result of the debate.
"I really feel that the NCT is moving into a whole new phase of its development. If they don't feel comfortable with that, they have to follow their conscience."