The whips' role in the sacking of Sir John Wheeler and Nicholas Winterton from select committees has caused an outcry among the old guard which is expected to continue this week, with appeals to the Speaker to intervene.
But potentially more worrying for the Government is the rift with some of the new Tory MPs, who signed a 'rebel' Commons motion on 3 June after the rejection of the Maastricht treaty in the Danish referendum.
The fear that careers may have been marred as a result of putting their names to early day motion (EDM) 174 - on 'future development of the EEC' - is still eating away at a few of the new intake. Their resentment is directed at one whip, David Davis, who is regarded as the main 'enforcer' for Richard Ryder, the chief whip, and whose approach contrasts with the more lumbering style of David Lightbown, the former backbench hate figure in the whips' office. Some of the troops are now calling for a 'truce' and a fresh start before the House rises for the summer recess.
The unrest began immediately after the election, when the whips called the 'Class of 92' to a meeting in a Commons committee room for a lecture on discipline by David Heathcoat-Amory, the deputy chief whip.
An urbane former parliamentary aide to Douglas Hurd, he was mild-mannered, but the meeting backfired, even among some of John Major's most loyal friends, because it was seen as outmoded.
'It was ridiculous. Some of those present, like Paul Beresford, had been running authorities. They didn't want to hear do's and don'ts,' said one former ministerial aide.
Another Tory MP complained: 'They treated us like a bunch of kids on their first day at school.'
There was a feeling among the whips before the new intake arrived that some had to be cut down to size. EDM 174 was the opportunity. It was led by a former minister, Michael Spicer, and cleverly sought to conceal its rebellious nature by calling for the ratification of the Maastricht treaty to be postponed to enable a 'fresh start' to be made.
Twenty-six of the 62 Tory MPs in the new intake signed it. They included: three former advisers to Margaret Thatcher - Hartley Booth, David Willetts and John Whittingdale; members of the supposedly Majorite 'Standard Bearers' including Mr Willetts, Alan Duncan, and Liam Fox; and others, such as Lady Olga Maitland and Nirj Deva, chairman of the Anglo-Asian Conservative Association, who had close connections with Conservative Central Office.
'We thought it was helpful to the Prime Minister. Maybe we were a bit naive, but it was never intended to oppose John Major,' said one of those who signed.
Michael Fabricant said the whips acted on him like 'Starsky and Hutch', one cajoling, the other threatening. Lady Olga and Mr Booth withdrew their names.
It was no surprise that it was signed by well-known anti-federalists in the new intake, such as Mr Whittingdale, Bernard Jenkin, the son of Lord Jenkin, and Iain Duncan-Smith, who took over Lord Tebbit's Chingford constituency.
Mr Jenkin has become the target of some of the whips, who regard him as 'beyond the pale' on Europe. But some whips also view other members of the new intake, such as Mr Willetts, a genial intellectual, as 'too clever by half'.
Others who were conspicuous by their absence included Judith Chaplin, Mr Major's former political adviser. She urged her friends not to sign the motion.
The Prime Minister privately made it clear he thought it was unhelpful at a private buffet lunch at Downing Street, as he toured the groups of invited new MPs. Some emerged shell-shocked from the experience.
'He should have told us that he understood how we felt, and that it would not be a blot on our careers,' one complained.
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