Earlier, following a meeting at Downing Street, Mr Thurnham appeared to have bowed to pressure from party chiefs to reconsider his position over the weekend. But later, after "reflecting further" he decided to go ahead and resign.
Mr Thurnham's resignation represented a hammer blow to Government efforts to hold the line over Scott, as Sir Richard expressed irritation over the Government's presentation of his report and two more Tory MPs warned that Mr Major could not count on their support.
Sir Richard broke his silence to rebuke ministers for quoting him "selectively" in their defence. His blunt intervention forced the Government back on to the defensive in the increasingly bitter inter-party row.
Kenneth Clarke, the Chancellor, had already admitted that because of a "drafting error", the government press pack - issued on the day the report was published - wrongly claimed William Waldegrave, the Chief Secretary to the Treasury, had been found by Sir Richard not to have misled Parliament.
Instead, Mr Clarke told Labour's Treasury spokesman, Andrew Smith, the qualification "intentionally" should have preceded "misled".
The terse letter from the secretary to the Scott inquiry, Christopher Muttukumaru - authorised by Sir Richard - to Ian Lang, President of the Board of Trade, protested sharply at the "selective" use by ministers of only part of an answer given by Sir Richard at a press conference a week ago.
Ministers had relied upon Sir Richard's phrase that it was a "fair summary" of his findings to say that there had been "no conspiracy and no cover-up" over the sale of arms-to-Iraq.
But the judge - now Vice Chancellor of the Chancery Division - asked Mr Muttukumaru to point out to Mr Lang that after this phrase he had immediately added: "Any soundbite answer, any summary one-line answer is bound to be a distortion of what I have taken care to express in the report."
The sharpness of the note, sent to Mr Lang's Principal Private Secretary, John Alty, underlines what is believed to be the increasing annoyance felt by Sir Richard and inquiry staff at the aggressively partisan way in which the Government has presented the findings.
Meanwhile Quentin Davies, a member of the Commons Treasury Select Committee and the MP for Stamford and Spalding, startled some MPs at the weekly meeting of the 1922 Committee by expressing strong concern over Sir Richard's findings that Parliament had been misled by repeated answers over arms exports.
Mr Davies last night met Alastair Goodlad, the Tory Chief Whip, to discuss his concerns. Meanwhile, John Marshall, the MP for Hendon South, writes in today's Jewish Chronicle that he has not yet made up his mind about the affair, and that the Government must "address the concerns" raised by the Scott report.
Sir Richard's letter was sent soon before John Major again told the Commons, in an answer to the senior Liberal Democrat, Malcolm Bruce: "Sir Richard has agreed that there was no conspiracy, no cover-up". And it follows a string of statements by Cabinet ministers - including Michael Howard, the Home Secretary - alluding explicitly to this remark by Sir Richard.
The report criticised Sir Nicholas Lyell, saying he was wrong to advise ministers they had a duty to sign Public Interest Immunity Certificates and that he failed to pass on fully the strong reservations of Michael Heseltine, President of the Board of Trade, about signing these. He also says there was a deliberate failure to give Parliament information about changes in arms export guidelines, but exempts Mr Waldegrave from "duplicitous intent".
Downing Street was dismissive yesterday of the letter
Inside Parliament, page 7