The allegations came in a reaction to the Queen's Speech from the Directory of Social Change, which said it was "dismayed" the commission wanted to confine consultation to the main umbrella and representative bodies.
"There is no mention of taking into account the views of any other persons or bodies, such as those whom this public benefit is supposed to serve," said a statement from the DSC.
But Rosie Chapman, director of policy at the commission, said this was "mischief-making" and that there would be wide public consultation as part of establishing an overall framework for applying public benefit tests.
"But then would come the question of how to apply the tests to particular sectors, and of course everyone is thinking first of the independent schools," Chapman added. "At that stage, we would need to speak to the umbrella bodies in that sector. The NCVO would be included, and the DSC would probably be a standard consultee.
"We will be getting a full spectrum of views, not just the vested interests. As well as consulting the charities, we will be talking to the people who benefit from them. We are still working out these proposals, and it's good if people want to engage with that - but misrepresentation is not helpful."
Chapman said consultation with the public was a key factor, but the legal framework was important too: "If you relied entirely on public consultation, organisations involved in, say, asylum and mental health might not be charities."
The inclusion of the Charities Bill in the speech was widely welcomed, but Acevo chief executive Stephen Bubb said the story was not yet over.
"The challenge for charities is now to make sure this Bill is given legislative priority and made law before the next General Election," he said. "We also need a Treasury Bill to free up charity trading. Current rules are an unnecessary straitjacket for enterprising charities."
The inclusion of the Disability Discrimination Bill was greeted with reservations, partly because its announcement was delayed by the Parliamentary row over hunting. John Knight, head of policy at Leonard Cheshire, said: "Delaying our civil rights to score political points over hunting is disgraceful."
The National Autistic Society welcomed the Bill but said it should include a specific clause so people with autism were properly protected by it.
Peter Cardy, chief executive of Macmillan Cancer Relief, called for the Bill to be changed so that people diagnosed with "minor" forms of cancer were not excluded from cover.