Moneysupermarket.com has claimed analysis shows that fees for fixed and tracker mortgage products have increased by over 13% since September 2009.

It has warned borrowers that, once fees are factored in, a product with a slightly higher rate but lower set-up costs may actually prove cheaper than low headline rate deals which often incur high fees.

The comparison site cites, for example, the lowest two-year fixed rate is from Santander at 2.79% however, this includes a combined booking and arrangement fee of £1,995, meaning the total amount to be paid back over the two years for someone borrowing £150,000 is £18,676. The same amount borrowed over two years with Royal Bank of Scotland at a rate of 2.99 and a fee of only £499, would cost £17,552 – a saving of £1,124 over the two year period, despite the interest rate being 0.20 percentage points higher.

Clare Francis, mortgage spokesperson at moneysupermarket.com, said: “When looking for a new mortgage