The charity, which supports people with ME - also known as chronic fatigue syndrome - said that its 7,673 fee-paying members were not entitled to vote at AGMs because they were not members in a legal sense.
A Charity Commission spokeswoman said it had dismissed a number of complaints on the issue between 2003 and 2005. "We were satisfied that there had been a misunderstanding," she said.
The dissident members claim that the charitable company, which broke away from the ME Association in 1994, is acting unconstitutionally because it does not hold AGMs or represent members' views.
A group of about 16 demonstrated last week outside a conference at the Royal Society of Medicine, where the charity's chief executive, Sir Peter Spencer, was due to give a speech. They claimed the board of AfME had become dominated by people who believed ME was a psychological condition. Most ME sufferers, they said, believed it was physical.
"Only by re-establishing the democratic link between AfME and its membership will AfME gain a mandate to speak and act on behalf of us," said Ciaran Farrell, a member of AfME. "Filling in a questionnaire is not the same as being able to vote on policy or elect trustees who see things your way."
Richard Evans, trustee and company secretary of AfME, said the charity's website made it clear that "being a member of AfME, the organisation, is not the same as being a member of Action for ME, the company limited by guarantee, as a company law matter".
He said the charity's latest AGM had been held in February and that trustees, who are the only legal members, had been invited.
A spokeswoman added that AfME required the majority of its trustees to have had ME, and that all but two of the current 10 board members were either sufferers or carers. She said the disgruntled group had been campaigning against AfME for many years.
Governance expert Judith Rich said charities should hold regular meetings with their memberships regardless of whether it was legally required. "That is the only way charities can be sure they are truly representing the views of their members," she said.