The comparison site looked at how 18 of the UK's leading mortgage lenders handled arrears issues; including missed payments, returned cheques or direct debits and debt counselling.
It found that there was a growing gulf between they way lenders dealt with the difficult issue of arrears.
Northern Rock and BM Solutions for example both give borrowers one month's grace for a missed payment, however GMAC-RFC charges them £50 from the get go.
HSBC on the other hand do not levy a charge for any of the named areas of investigation.
In total, Cheltenham & Gloucester borrowers would be charged £372 if they had a returned cheque or direct debit, three months arrears and then scheduled an arrears advice appointment on top.
As well as these extra charges, moneysupermarket.com also found that some lenders, such as the Halifax, charge interest at a higher rate on the arrears.
Louise Cuming, head of mortgages at moneysupermarket.com, said these charges were both 'punitive' and 'unjust' and simply burdened customers with more debt.
"Many lenders are quick to agree on a mortgage, but not so eager to help financially when their customer is most in need," she added.
"Charging someone £372 is equivalent to raising the annual SVR rate on a £150,000 mortgage from 7.5 per cent to 8.49 per cent.
"We would question if these lenders are treating customers fairly, given the inconsistency of the fees and charges - under the Mortgage Conduct of Business rules, all cases of financial hardship must be treated sympathetically.
"The biggest outrage is that so many lenders charge for or outsource debt counselling, yet it is free with the Citizens Advice Bureau."
