"We need to develop some new instruments, which sit somewhere between interest rates, which affect the whole economy... and individual supervision and regulation of individual banks," he said.
"We need to develop something which bridges that gap and directly addresses the financial cycle and prevents the financial cycle and the credit cycle getting out of hand."
Commercial future
Sir John has specific responsibility for financial stability.
He was savaged when interrogated last autumn by the Treasury Select Committee for allegedly being insufficiently on top of the crisis at Northern Rock. His colleagues regarded the attack as unfair.
In his BBC interview, he cast doubt on whether the exchequer would get all of the money back that it has pumped into the banking sector.
"There are some books: Northern Rock, Bradford & Bingley, which the taxpayer's now holding, which clearly have a level of defaults in them, [I'm] not quite sure how that will balance out against the residual of the capital," he said.
"As for the more mainstream banks, yes I think they've got a commercial future and I'm sure that in time they will... revive and start building and growing as commercial entities again."
Meanwhile, the boss of Barclays bank tells the programme that consumers and companies will continue to find it difficult to access credit for the next one to two years.
Panorama: The Year Britain's Bubble Burst, BBC1 Monday 22nd December at 2030 GMT
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