The disclosure, by a former Government whip, that Tories disposed of their private notes will raise serious doubts about the freedom of the committees from party manipulation.
New select committees were established last week to represent the balance of MPs in the new parliament.
The disclosure also underlines the extent to which the whips interfered in investigations into sleaze by the former Standards and Privileges Committee for its report on Neil Hamilton and allegations of payments by Mohamed al Fayed, the owner of Harrods.
The Tory Government whips' office became alarmed when Mr Willetts, then a Government whip, was investigated for writing a note to Alastair Goodlad, the then Chief Whip, disclosing conversations he had had about the proceedings of the inquiry into sleaze. Mr Willetts was later accused of "dissembling" in his replies to questions from the committee about the note he sent to the Chief Whip.
The Independent has learnt that, within a week of the inquiry, the Tory whips destroyed all other notes they had on file. A former government whip said: "They waited a few days and then destroyed the lot. I think they shredded them. They were worried they would be called to give them up to the committee.
"Everyone thought it was very harsh on David Willetts. All he was doing was his job. It is part of the game. Everyone knew what the whips were up to."
There have been continuing complaints about the intrusion of the whips in the select committee system. Tory members of the former health committee, then chaired by Marion Roe, a former Tory minister, were accused of passing their reports and amendments before publication to Virginia Bottomley, then Health Secretary, with the approval of the whips.
Mr Hamilton, who is still protesting his innocence, complained in a note to the Standards and Privileges Committee that he had been a victim of the whips.
The former minister for Corporate Affairs cited Mr Goodlad's predecessor, Richard Ryder, in his evidence to the committee inquiry for allegedly refusing to allow him to see Michael Heseltine, then President of the Board of Trade, and his Cabinet boss, to answer the allegations. He was also denied permission to communicate to other colleagues in the Commons. "The Chief Whip refused to give me permission for this and told me to `go back to my department and get on with my job'. He did not tell me that it had already been decided that by lunchtime tomorrow I would not have that job."
Labour whips insist that they did not keep copies of notes sent to Derek Foster, the Labour Chief Whip in Opposition. "We just committed everything to memory. It was all done word of mouth," said a former senior Labour whip.
Parliamentary whips are often accused of practising "black arts" against MPs to impose discipline, but this appears to be the first time they have been accused of deliberately trying to avoid investigation by a Commons select committee.Reuse content