Political scholar Michael Pinto-Duschinsky said he has been forced to resign from a commission set up last year by Prime Minister David Cameron to investigate whether a British Bill of Rights could be established.
The Bill would replace the Human Rights Act which currently enshrines the European Convention of Human Rights in UK law.
Mr Clarke, the Justice Secretary and a pro-European, has said he doesn't see the need for the Bill. But the Conservative Party remains committed to scrapping the Human Rights Act, with powers repatriated to Westminster.
Today Mr Pinto-Duschinsky claimed Mr Clarke and the Deputy Prime Minister had tried to nobble the commission so it found in favour of the "status quo".
Speaking to the BBC's Andrew Neil, he said the commission had been consistently directed "away from consideration of parliamentary over-ride": handing more powers back to MPs in Westminster.
He added: "After one year it is now clear that it has been intended all along to issue a report in favour of the status quo.
"We have actually considered the question of parliamentary sovereignty only once in the whole year that we have been in existence.
"The commission answers to Ken Clarke. He and Nick Clegg set it up and selected the chairman. His civil servants run the commission and staffing. His hands are everywhere."
He added: "He (Ken Clarke) is following the agenda of the human rights establishment which is well represented on the commission. In doing so he is sidelining not only Parliament but also the Prime Minister, and I consider that disloyal.
"The commissioners were called in last December by Ken Clarke and Nick Clegg and told in (no uncertain) terms that we should ignore what was called agitation from parliament.
"Now I consider a 10-to-one vote - an overwhelming vote by our House of Commons - cannot be dismissed as agitation, and I said so."
A spokeswoman for the Commission on a Bill of Rights said it was making "good progress".
She added: "We have already discussed the issues of parliamentary sovereignty and democratic over-ride at length.
"The commission will issue its final report to Government by the end of the year in accordance with its terms of reference."