NHS Alliance has instigated a competing listening panel to that put together by the government for the Health and Social Care Bill.
It believes GP consortia are being left out of the coalition's own listening exercise as only five of the 40 members represent GPs.
The body, which represents GP Consortia, Primary Care Trusts (PCTs), clinicians and managers in primary care, commissioned the Listen Up exercise to "give clinical commissioners all the support they can get and ensure that their opinions are heard".
This will "ensure consortia have a prominent voice at a time when there is a lack of real representation and a lot of confusion among those who are supposed to take clinically-led commissioning forward," it added.
Dr Michael Dixon, chairman of the NHS Alliance, said there was no going back on clinical commissioning and the political discussions will not bring significant changes to this aspect of the bill.
"We are encouraging all GP consortia, especially pathfinders, to continue their pace of development and to not be distracted by the current hiatus in the passage of the Bill," he said.
"It is undeniable that we need to listen to all professionals involved in making clinically-led commissioning happen, including nurses, allied professionals and consultants. But, to be meaningful, this listening exercise needs to be led by frontline commissioners.
"It is about time that commissioners' voices are truly heard and that is what our listening exercise will do," he added.
