The Prime Minister told MPs that Mr Mates had resigned to avoid causing further embarrassment to the Government over continuing reports of his links with Asil Nadir, the fugitive businessman.
It was the leaking of a letter from Mr Mates to the Attorney General about an SFO investigation which forced Mr Mates out of office. But the manner of Mr Mates's reluctant departure left Tory MPs angrily accusing John Major of 'lack of leadership' and 'drift' in his government.
In his resignation letter, Mr Mates referred to the watch he had sent Nadir bearing the message: 'Don't let the buggers get you down.' He told Mr Major: 'In retrospect, I rather wish I had sent the watch with its now famous message to you.'
The Tory benches were stunned when the resignation was announced. Some who had called for his sacking looked sickened when it came.
Senior Tory MPs complained that Mr Major appeared to be waiting for the Tory backbench 1922 Committee to deliver the coup de grace at its weekly meeting last night. 'He should either have stood by Mates, or sacked him. There is complete lack of command,' said one of Mr Major's former leadership campaign team.
'He spent five days dithering about the future of one of his ministers, only to force him into his own decision in the face of a kangaroo court of Tory backbenchers,' said Paddy Ashdown, the Liberal Democrat leader.
Mr Mates spared Mr Major further embarrassment by telling him an hour before Prime Minister's Questions in the Commons that he would go. The Prime Minister said Mr Mates had acted 'with complete propriety' in raising Nadir's case with the Attorney, Sir Nicholas Lyell. He told MPs Mr Mates had resigned because of the embarrassment being caused to the Government. 'On these grounds, and on these grounds alone, he asked me if he could stand aside from his duties. With regret, I have accepted his resignation.'
While the letter to the Attorney General was not damaging in itself, it was seen by some of Mr Mates's friends as a 'shot across the bows' - carrying the clear threat that more damaging letter leaks were in the pipeline.
Peter Temple-Morris, MP for Leominster, said: 'It's obviously come from within the reaches of Government, its investigative authorities, or its prosecuting authorities of one sort or another. That's obviously where it's had to have come from.' Another backbench friend of Mr Mates was most concerned about the 'dark issues' raised by 'the SFO's coup de grace'. He said the calculated leak would serve as a warning to all ministers and MPs not to criticise the handling of SFO cases in future.
Other senior Tories, however, were more concerned with the role the press had played in bringing Mr Mates down. While Mr Temple-Morris said it had been used 'for someone else's end', Tom King, former Secretary of State for Defence, complained: 'A rampaging press, without responsibility, can obviously do great damage to our society.'
Dame Jill Knight, an executive member of the Tory backbench 1922 committee, said the resignation was 'sad because the press will once more be given the idea that once they target someone, it is merely a question of time before they go'. That concern - that ministers such as David Mellor, Norman Lamont and Mr Mates were being picked off by a prowling press pack - exposed an underlying party criticism of Mr Major's weakness in the face of attack.
He was accused of 'throwing vulnerable ministers to the wolves', and having fed their appetite, the question was being asked: 'Who is next?' Norman Fowler, the party chairman and one of Mr Major's key political advisers, was one of those nominated.
While some ministers and MPs defended the Prime Minister, saying that there was never a right moment to demand a resignation, Sir Trevor Skeet reflected the view of others when he said Mr Mates should have gone much earlier, and it was a pity that backbench MPs were being left to force ministers out.
Last night for the first time, Nadir, who paid the Tory party pounds 440,000 through his companies, claimed Kenneth Baker, then party chairman, complained to him about a lack of party funds. Mr Baker, who had denied that allegation, has told the Independent they had discussed the presentation of the poll tax policy.
In last night's New at Ten interview, recorded on Wednesday, Nadir said: 'He explained the reason why some of their policies were not being put across properly or as they wished was because of the lack of funds.' Nadir said he was 'heavily courted' by Tory leaders, including Mr Baker, whom he met at Central Office.