Fees for fixed and tracker mortgage products have risen by over 20% since September 2009, according to analysis by MoneySupermarket.

This, the comparison site says, is making it more difficult for borrowers to compare the true cost of mortgages.

MoneySupermarket says that, for example, the lowest two-year fixed rate mortgage is from HSBC at 2.64%, however adding the combined booking and arrangement fee of £1,999 means the total amount to be paid back over the two years for someone borrowing £150,000 is £18,404.20. The same amount borrowed over two years with Bank of Ireland at a higher rate of 2.78%, and a fee of only £799, would cost £17,461.48 – a saving of £942.72 over the two year period, despite the interest rate being 0.14 percentage points higher.

“It’s very easy for borrowers looking for a new mortgage to be attracted by low headline rates; however it is vital to consider the account arrangement and booking fees as part of the overall cost,” said Clare Francis, mortgage spokesperson at MoneySupermarket.com.

“Fee costs can vary greatly between providers so taking the time to work out the total amount you have to repay over the term of the offer is essential.

“That said, for some people it may be worth paying a high fee in order to benefit from the lowest interest rate. It will all depend on the amount you are looking to borrow – on large mortgages a high fee can be worth paying in order to secure a low rate. However, with smaller mortgages, where a high fee will form a larger proportion of the overall loan size, it may work out cheaper to keep the set up costs low even if it means paying a slightly higher monthly payment.”