Billionaire Michael Ashcroft on Tuesday started libel proceedings against The Times newspaper, which has raised repeated questions over his integrity and business dealings.
The charges were repeated in Parliament on Tuesday by Labour MP Peter Bradley.
The newspaper has denied any conspiracy against Mr Ashcroft, who is the Tories biggest single funder and has given the party about £3m in recent years.
But, speaking to BBC News Online, Mr Ancram said: "I think there has been a clear politically-motivated campaign in which The Times newspaper has played a part.
"We see today they are using the cloak of parliamentary privilege to make innuendoes and assertion about Michael Ashcroft on their front page and on their inside page they're telling people in Eddisbury to vote Labour and I think there is no coincidence between those two things happening."
No need to repeat allegations - MP
The Tory chairman confirmed the party was not backing its treasurer in his legal action, but insisted it would not allow anyone to be driven from office by "rumour and innuendo".
Mr Ancram said: "The legal action is his legal action. He had to make up his own mind about that given the legal advice he was receiving.
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"I've said for some time that I believe there is an organised smear campaign. The motivation for it is unclear."
Mr Ashcroft himself described articles in the paper in recent days as "perhaps the most one-sided, partial and coloured account of anyone's affairs ever produced by a newspaper in a free country".
He also challenged Mr Bradley to repeat the allegations he raised outside the House of Commons, where he would not enjoy parliamentary privilege protecting him from legal action.
In the Commons on Wednesday, the Labour read from files, which he said came from the US Drug Enforcement Agency (DEA), the Federal Bureau of Investigations and the International Narcotics Bureau.
He told the BBC on Thursday that he saw no need to repeat the allegations, as what he was said was contained in Hansard and had been broadcast.
"I was certainly not prepared to stand up in the House of Commons and say the things that I did if I was not convinced there was a basis for them and a justification for them," he added.
Times defends its investigation
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The Times' editor, Peter Stothard, defended his actions, saying claims of conspiracy were only serving to divert attention away from the substance of the allegations.
He said: "We are involved in a serious long-term investigation in to a matter of high public interest - the treasurer of the Tory party and his business and political background and his role in our public life.
"That is the substantial main point of what The Times is doing and what the editor of The Times is doing.
"Everything else is just spin put on by Conservative Central Office and friends of Mr Ashcroft attempting to draw attention away from the absolute substantial point of these allegations because Mr Ashcroft lies at the heart of an unregulated banking system in the Caribbean."
Michael Ancram answers your questions
(22 Jul 99 | UK Politics)
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Ashcroft: The Tories' troublesome tycoon
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