Liddle found himself on the receiving end of a public dressing down after he was critical of the countryside marches in his Guardian column.
The attack was led by the Daily Telegraph, which published an editorial on what Liddle had written, and accused the 'Today' programme under Liddle's editorship of failing to properly cover the Countryside Alliance story.
In the Guardian column, Liddle attacked public schools that reportedly encouraged pupils to go to the rally.
He wrote: "You may have forgotten why you voted Labour in 1997. But then you catch a glimpse of the forces supporting the Countryside Alliance and suddenly, rather gloriously, it might be that you remember once again."
Liddle ultimately fell foul of new BBC guidelines for journalists, which state that they must not write articles that could undermine the BBC's impartiality.
In an earlier statement issued last week, the BBC said the piece was "not acceptable" and "does not square with the BBC's obligation to be impartial and to be seen to be impartial". Liddle had accepted the column was a "significant error of judgement".
The corporation said that Liddle will now work on a pilot for a new programme about politics for TV station BBC Two. He is also discussing other presenting roles he will take up with the BBC.
Richard Sambrook, BBC director of news, said: "I have been talking to Rod for several weeks about a new role in BBC News. We both agreed this is a good time for him to move on from 'Today'."
He added: "Rod is one of our strongest editors and I have great admiration for what he has achieved on the programme over the last five years. Under his editorship, 'Today' has been extraordinarily successful."
The BBC will be advertising for a new editor in the next couple of weeks.
Liddle took over as editor of the 'Today' programme in 1998 and oversaw its expansion to three hours from 6am. In the first half-hour, there is now an early morning briefing beginning with the news headlines, developing the main story of the day and frequently covering a foreign story.
The Liddle CV
1990 Assistant editor, 'The World This Weekend'
1993 Assistant editor, 'Today'
1996 Editor, 'The World Tonight'
1997 Deputy editor, 'Today'
1998 Editor, 'Today'
2002 Resigns as editor of 'Today'
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