The teams often met after a day's play in the series, which England won 2-1, and Waugh felt it contributed to the Australians' surrender of the Ashes for the first time in 17 years.
But Warne said: "It has not got anything to do with it. If we had batted a bit better then we would have done better.
"We have been pretty successful, apart from one series, and you can read too much into it. It is easy to sit back when you are not playing and say we should be doing this and should be doing that. There is no disgrace in getting beaten by a better side."
Warne, currently captaining Hampshire in the English County Championship, also claimed that England should not go down the route of having separate captains for Test and One-day cricket.
Michael Vaughan's knee injury could see him give up the shorter form of the game so England would have to appoint another skipper, probably Andrew Flintoff, for the one-dayers.
Australia had two captains towards the end of Waugh's reign with Ricky Ponting taking over for the limited overs internationals and Vaughan's record in one-day cricket is far inferior to his Test record.
However Warne said: "Two captains can work as long as there is communication between the two then there is no drama.
"But I like having one captain. It should be a treasured position and he should be someone all the guys look up to. Two can work but one is better.
"Michael Vaughan is a very good player and a very good captain, he's very aggressive and he's got all the shots and is a very important part of the team. But he has got to perform and be worth his place in the side."
Warne was speaking as he signed a new five-year sponsorship deal in London. As part of the contract, he will head up a search throughout England for young spin bowling talent. Eventually he will undertake a similar project in other parts of the world.
And Warne, who has 685 Test wickets, is not worried if any of his proteges bowl England to an Ashes victory in the future.
He added: "If that's the case then that's great. I want to see spin bowling go on and on and on. In England there is a lack of spin bowling and a lot of that is down to the attitude of captains who always revert to the medium-pacers with one slip, a third man and a ring field.
"The most exciting things in cricket are fast bowling or a spinner with someone like Kevin Pietersen coming down the wicket to them and trying to slog them for six. There is nothing wrong with being hit for six - you always get the ball back and you can have another go."