"Never before have we seen so much anger in our sport in Great Britain," said BEF chief executive Andrew Finding, who described the situation as a crisis.
Finding was commenting amid the furore which has been growing since the FEI General Assembly adopted the progressive list, allowing low levels of several therapeutic drugs in a horse's system during competition, including phenylbutazone.
The British federation said it was deeply disappointed that the debate over the progressive list had "completely overshadowed" the FEI's Clean Sport initiatives, which it applauded.
However, it said it was "deeply concerned" by the adoption of the progressive list.
"The 'progressive list' was sent to the national federations of the FEI on Friday, November 13, just six days before the day of the General Assembly on Thursday, November 19.
"There was no time for consultation, effective global debate or consideration of the serious implications of the dramatic policy change placed before the General Assembly.
"We have doubts about the legitimacy of the vote taken in light of the failure in timely notification of the resolution in question," the BEF said.
"We do not believe that all national federations could have been alert to the vital issues for the future of our sport when they were asked to vote on the earlier list, sent to national federations on October 20 (subsequently renamed the 'Current List' which added further ambiguity), and the later 'progressive list'."
It urged the FEI to either defer the introduction of the list to allow timefor more consultation - which the FEI Bureau did earlier today (NZ time) - or withdraw permissibility of the drugs on the progressive list.
Finding said it was saddening that the good work undertaken by the FEI in Clean Sport had been overshadowed in such a way.
"Of course, there are differences of opinions amongst nations and within in the FEI; it could not be otherwise in a highly competitive sporting body.
"The majority of nations present voted in favour of the 'progressive list' and we must respect the democratic processes, but on this occasion, the proposal was bounced on national federations at unacceptably short notice and so we have a deeply flawed decision and a crisis of confidence on our hands.
"There is a universal demand from our community in Great Britain for change or amendment to the 'progressive list'.
"While this crisis unfolds and a satisfactory conclusion is sought, we encourage our sporting bodies, welfare groups, show and event organisers and their sponsors to maintain their programmes and plans in place.
"We will continue to use all means at our disposal to impress upon the FEI the necessity for change and will accordingly work with our partner national federations in Europe and elsewhere.
"We have established a small working group of experts to consider the issues at hand, to monitor developments and provide advice. We will publish a set of recommendations for publication that covers all of the implications of the Clean Sport initiatives shortly."