Two panels of teachers, employers and academics, consulted by the Qualifications and Curriculum Authority for the past five years on policy proposals, are being disbanded.
The moves are part of a radical shake-up of the QCA, instigated by Dr Boston after he became chief executive last September, which has also seen 16 senior managers replaced.
Members of the curriculum and assessment committee were not aware of the move until last week's meeting, which proved to be its last.
Dr Boston apologised the next day for the handling of the abolition, saying it had been a "serious mistake".
Ted Wragg, a QCA board member and TES columnist, wound up last week's meeting. One committee member said: "Ted Wragg ended the meeting by thanking us all for our sterling work.
"We looked at each other and I was asked 'did I know that this was the last meeting?' None of us knew about it. There must have been a communication breakdown."
Stephen Ball, head of Ivy Bank Business and Enterprise College, Burnley, said: "Over the past five years, this committee has produced high-quality policy advice, and it saddens me to think that that voice may not be heard by the authority."
Dr Boston has admitted in an email to what "must have seemed very heavy-handed action on my part". He thought committee members knew about the changes.
The 11-member qualifications committee is also being wound up. The committees were set up by Dr Nick Tate, the former QCA chief executive, to ensure that external "stakeholders" influenced the policy-making process.
The QCA said although these two panels were being replaced under the reorganisation, there would continue to be a place for independent advisory committees at the QCA.
There would be a growing voice for external opinion, and many of those serving on the groups would find a place in the new structure.
A paper setting out recommendations for a new committee structure is to go to the QCA board later this month.