The Tory chairman has threatened the BBC with a cut in its licence fee if it doesn't become more transparent.
Grant Shapps said the corporation had to tackle waste and secrecy if it is to justify its public subsidy.
In an interview with the Sunday Telegraph, Shapps claimed there was a "question of credibility" for the BBC over whether it applied "fairness" to its reporting of politics, and raised concerns about a "particular journalist" - thought to be Home Affairs editor Mark Easton.
Speaking on the BBC's Marr show on Sunday morning, former BBC director general Greg Dyke accused the Tories of strong-arming the corporation ahead of the next general election.
"It's putting a marker down for the election," he said.
Labour deputy leader Harriet Harman claimed that "some Tories are against the BBC because it’s a public corporation, and they’ve never liked it".
With the BBC's royal charter coming up for renewal in 2016, Shapps suggested that there were "lots of different ways" in which licence fee-payers' money could be used to fund public service broadcasting.
And he said that the £145.50 annual fee would be "too much" if the BBC failed to reform.
He made clear Conservative frustrations with the current operation of the BBC.
"They have ended up working in this culture which is buried in the last century, which is 'we are the BBC, we do what we like, we don't have to be too accountable'," he told the Sunday Telegraph.
"But they are raising £3.6 billion through the licence fee, which is a tax, and, quite rightly, the public wants to have sight of how the money is spent. Things like the pay-offs have really caused concern, as have, obviously, things like
Savile and Hall and the culture that goes around that. I think it is one of too much secrecy."
BBC director general Lord Hall should consider opening the corporation's books to full inspection by the National Audit Office, publishing all expenditure over £500 - including stars' salaries - and opening up to freedom of information requests, he said.
"In order for the public to have confidence in the three-and-a-half billion (pounds) plus that is given to the BBC - compulsorily, just because you have a television - and to move beyond Savile and the pay-offs and all the rest of it, the only way they can do that is to really go for a much more transparent, open deliberate policy," said the Tory chairman.
"If they do that they can make sure they win back public trust. If they don't, they are in danger of frittering away Auntie's public trust that has been built over a long time."
And he indicated he was ready to contemplate change in the system which has so far seen the BBC take all of the money raised through the licence fee.
"People pay their licence fee in this country because people believe that we should have public service broadcast programming," he said.
"Of course, there are lots of different ways you could do that.
A BBC spokesman said: "Mr Shapps is right that transparency is key to the future of the BBC. So is its freedom from political pressure."
He added: "Mark Easton is one of our most experienced and well-respected journalists with a long track record in reporting without fear or favour."
The spokesman defended a feature by Easton on a recent European Commission report about immigration, which Mr Shapps maintained was "wrong".
"We are satisfied that our coverage of the European Commission report was fair, balanced and impartial," said the BBC spokesman.
"As we do with all our stories, we explored the wider debate with relevant context and represented a range of views.