David Davis claimed Gordon Brown had "gagged" ministers by ordering them not to debate civil liberties ahead of the Haltemprice and Howden by-election.
The former shadow home secretary, who resigned his seat earlier this month over the controversy surrounding 42-day-pre-charge detention for terrorism suspects, accused the Prime Minister of stifling democracy.
But Labour immediately hit back and dismissed the senior Tory's assertions as "deluded".
The row flared after Labour refused to put up a candidate for the July 10 by-election Mr Davis has forced in a stand against what he terms the Government's erosion of civil liberties.
Mr Davis said: "Gordon Brown's cowardice has plumbed new depths. First he refuses to put up a candidate against me in the by-election. Now I am told that he is gagging ministers from engaging in debate about the Government's erosion of our historic rights and liberties.
"Mr Brown is happy to sanction attempts by ministers to damage my case through smears and innuendo. But he cowers in Downing Street refusing to debate the issues and instructs his ministers to follow suit. His stance is contemptible and undemocratic."
But Mr Brown's aides insisted there was no truth in the claims.
A Number 10 spokesman said: "This is totally untrue. In fact the opposite is the case. We relish the chance to debate the issues around 42 days, the use of CCTV and DNA evidence."
Labour's refusal to take part in the by-election, on the grounds that it is "phoney" and a waste of money, has left Mr Davis with no serious opposition in the contest.
The Liberal Democrats are not taking part because they agree with Mr Davis on the issue of 42 days. Those who have thrown their hats in the ring so far include Mad Cow Girl from the Official Monster Raving Loony Party and a Northampton market trader.
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