Most Revd Justin Welby told the Campaign for Fair Finance initiative that some sites were not "genuinely fair", favouring companies paying higher rates of commission.
This goes against the idea of price comparison websites providing objective, impartial information so a consumer can make up their mind on which deal to go for.
Mr Welby also said the industry required "regulators breathing more heavily down their neck" to keep malpractice in line.
He told the Campaign: "Both parties in a deal have to decide they are going to play fairly so part of it is changing culture, part of it is things like comparison websites that are not skewed towards anyone."
David Barclay, the Faith and Public Life Officer at the Centre for Theology and Community, has led the Church of England's work promoting and creating credit unions and ensuring payday lenders do not exploit people who cannot repay their loans.
He told Premier: "[On] payday lenders, where the Archbishop has been really outspoken, that has led to really positive change. There was a real spotlight shone on the cost of their loans and the way they were doing business - good change in the regulations that has now seen problems with payday lending drop by about a half.
"The key point of a price comparison website is to give transparency. So obviously there's a problem there if in reality what they're giving is not a clear sense of the different options and where commission is skewing that choice for people that is clearly something that needs to be looked at.
"Clearly what the Archbishop is saying is that actually maybe we need to look a bit deeper at what's really going on, because they present themselves as open and transparent and if they're not in fact acting as such that needs to be scrutinised quite carefully."
Listen to Premier's Aaron James speaking to David Barclay here:
Premier has contacted price comparison websites and is waiting for a response.
The Association of British Insurers does not represent price comparison websites, however many products and companies it does represent are featured on those sites.
ABI told Premier: "As far as insurance is concerned, customers benefit from a very competitive market, enabling them to shop around for the best deal. Comparison websites can play a valuable role in helping customers compare policies and prices.
"What is important is that customers can accurately, and clearly assess the insurance products on offer to help them make the right decision for their circumstances, regardless of how they buy insurance."