This follows the DoH recommendation to the pay Review Body of a third pay freeze for GPs (GP, 9 November).
The BMA called for a pay rise of between 3.6 and 4.3 per cent for all doctors for 2008/9 in the first round of evidence submitted last month.
NHS Employers recommended a pay award of no more than two per cent, but was also unspecific about GPs.
GPC negotiator Dr Richard Vautrey said: 'We should not assume that what the DoH says will form the outcome of this process. It doesn't mean that it is the end of the story.'
The BMA has prepared and submitted its supplementary evidence to the pay Review Body.
Dr Vautrey described it as 'robust evidence that counters arguments' in DoH evidence.
He added that 'a number of very alarmed GPs' and 'doom-mongers' believed a pay freeze was inevitable.
GPC chairman Dr Laurence Buckman said the Doctors and Dentist Review Body had in the past made decisions against the DoH's evidence and in some cases had 'come up with ideas that neither parties thought of'.
He said the BMA's newest evidence 'did a pretty good demolition job on what the government says it can afford'.
Discussions with NHS Employers about the recommendations to the pay Review Body were ongoing, and proceeding 'amicably,' Dr Buckman said.
'There are cynics out there who say what the DoH says is final, but we will be as persuasive.'
All supplementary evidence will be submitted by early December before oral evidence.
The Review Body is expected to give a report to ministers in February 2008 before a March 2008 publication.