Its research showed that the average arrangement fee has risen £151 over the past 12 months, with the highest flat fee on the market £3,800 charged by Accord Mortgages.
Precise Mortgages has the highest percentage fee at 2%.
By comparison, the average mortgage arrangement fee was £879 in August 2010.
Moneyfacts found that just 12%, or 357, of all mortgages charge no arrangement fee.
Michelle Slade, spokesperson for Moneyfacts.co.uk, said: “Lenders appear to be offsetting the low mortgage rates on offer by increasing the arrangement fees.
“The average arrangement fee has increased by 17% as lenders battle it out to offer the lowest headline rate.”
She added that percentage fees have become increasingly common and too many borrowers still focus on getting the best initial rate, without fully considering the true cost.
Slade said: “In many cases, a low rate with a high fee can work out more expensive than opting for a slightly higher rate, but with a lower fee.
“12% of mortgages charge no arrangement fee and many of these regularly appear in the Moneyfacts best buy tables, which are based on true cost.
“With 2,873 mortgages available there is a raft of rate/fee combinations for borrowers to consider.
“The key to deciphering the maze of thousands of mortgages and getting the best deal is for borrowers to do their homework and shop around.”
