The protest came from Sir Henry Plumb and Tom Spencer, who lead what is left of British Conservatives after their numbers were almost halved in the June European elections. Mr Spencer said: 'I think he was badly advised on this part of the speech.'
The Prime Minister had warned the two men that they would not like the tone of his remarks. But his dismissal of the body as an 'unrepresentative and rather incoherent range of parties', which could not make up the democratic deficit, came as a shock.
British Euro MPs now face embarrassment from right- wing political allies when the parliament reconvenes.
Mr Spencer said: 'If Mr Major is questioning the democratic legitimacy of our role then what are we doing here? He has only just worked very hard in the Euro elections on behalf of the Conservatives.'
Mr Spencer said he welcomed Mr Major's proposal for joint committees of MPs and MEPs to scrutinise European decision-making, but the timing of Mr Major's attack was 'not helpful'. He said he expected close questioning from colleagues within the European Peoples Party, the coalition of centre- right parties.
The letter urges Mr Major to get MPs to help remove the 'ignorance and sense of impotence' about the way the European Union worked. Downing Street said: 'The letter will be duly considered and they will get a reply.'
The episode risks souring relations between MEPs and the rest of the Tory party, which Mr Major has worked to improve after the departure of Baroness Thatcher.
The Prime Minister said in the lecture that the Parliament 'had a long way to go before it wins respect and popular affection.' It was a 'flawed ambition' for it to see itself as the future democratic focus for the Union.