The Match of the Day presenter was taken off air last March by the BBC after posting a tweet in which he said the language used to launch a UK government policy on small boat crossings was "not dissimilar to that used by Germany in the 30s".
Speaking at the Hay festival in Powys, Lineker suggested the real problem had been a critical front page headline from the Daily Mail which was a "distortion" of his original comment.
"The one thing I do regret is that it was a fallout between me and the BBC and it should have been a fallout between the BBC and the Daily Mail," he said.
"I think it is a great shame because it pretty much pitched me against the BBC, and I love the BBC. I don't think we shout our corner enough; we get a little too defensive, particularly with worrying about what's in the Daily Mail. They've got a raison d'etre and they wanted a story on the BBC.
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Parry: Premier League would be 'sterile' without EFL
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Players must cope with extra scrutiny, says Lewis
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