Anita Straker, former head of the key stage 3 and national numeracy strategies, has been appointed as a temporary maths "tsarina" to spearhead government attempts to boost the subject.
Mr Clarke, who has a Cambridge degree in maths and economics and who is a former maths lecturer, is taking charge of the meetings with a host of leading government education figures.
Insiders say he believes the maths crisis, highlighted in a damning independent report, is one of the most serious facing his department.
The Smith report, published in February, outlined a catalogue of maths failings over 20 years, from botched curriculum reforms to the failure of ministers to collect proper data on staff shortages. Responses being considered include a double maths GCSE, offered at two levels rather than the present three. Pupils may also have to study financial management.
However, the Advisory Committee on Maths Education, set up with ministerial blessing to advise on teachers' views, was not invited to the meetings.
Professor Peter Saunders, of the Joint Mathematical Council, said:
"Decisions are being taken which are absolutely crucial to the future of maths education, without the involvement of the maths community. What's going on?"
Mr Clarke has not yet published a formal response to the Smith inquiry.
Those close to him say that he is serious about reform and that the ACME members will be given a chance to influence changes as the proposals are developed.