The analysis revealed the average product fee had increased to £1,078 from £1,018 last year and the proportion of fee-free mortgages dropped from 42 per cent to a third.
Mortgage fees are now at their highest point since 2012 when it was £1,095, Moneyfacts said.
Jo Jingree, mortgage adviser at Mortgage Confidence, said it was getting more common to see bigger lenders charge fees of £1,500 instead of the usual £1,000 which was probably causing the uplift in the average.
She said: “It’s also happening with buy-to-let mortgages. There are still fee-free options available but there is a massive discrepancy on the rates.
“There is less choice but it’s a shame when it’s the best option for a client.”
Iain Sillett, mortgage specialist at The Right Mortgage, said he noticed some lenders were not offering fee-free options at all, causing them to not show up on his product searches.
“They eliminate themselves from the sourcing system.
“You get clients who are averse to paying upfront fees as with some, the fee is non-refundable. The house buying process is expensive enough without adding on the fees especially with increasing interest rates,” he added.
Heightened caution has pushed mortgage rates up following the reopening of the property market and according to the figures, the average rates for fixed mortgage deals, both with and without a fee, increased by 0.51 per cent and 0.46 per cent respectively since July.
The average rate for a fixed mortgage with a fee is now 2.8 per cent, while without one it is 2.74 per cent.
Over the year, the number of mortgages offering incentives such as free or refunded valuations and cashback have also dropped.
The Moneyfacts data showed that in March, 71 per cent of mortgages had free or refunded valuations, whereas that number stood at 69 per cent in November.
Furthermore, a quarter of deals now offer cashback, a slight drop on the 31 per cent available in March.
The number of mortgage products with free or refunded legals has risen however, accounting for 54 per cent of deals compared to 49 per cent in March.
Eleanor Williams, spokesperson at Moneyfacts, said: “Average rates and fees are increasing, but there are still a variety of options to choose from, including those that reduce the upfront cost.
“Deciding on the right mortgage deal comes down to more than just the initial rate available, so seeking independent financial advice would be wise.”