The punitive measures are forcing the borrowers deeper into serious debt, with up to 30,000 people already in arrears on their mortgages.
Subprime lender Start Mortgages imposes the highest surcharge at 1pc a month on the arrears balance, which works out at 12pc a year.
AIB imposes surcharge interest of 6pc APR (annual equivalent amount) on arrears, while Bank of Ireland charges a penalty of 0.5pc a month, or 6pc a year, on the arrears amount only.
Halifax, along with its sister operation Bank of Scotland (Ireland) charges €12 if a direct debit being used to make mortgage repayments is unpaid.
A mortgage holder with Start whose repayments are €1,500 a month will have €15 added to the outstanding amount with every missed instalment.
Another subprime lender, Springboard, imposes a fixed charge of €15 a month for every repayment outstanding.
Noeline Blackwell, director general of Free Legal Aid Centres (FLAC), said imposing penalty charges is adding hugely to the overall debt people in arrears have to pay.
In addition, borrowers are also being charged up to €45 when lenders send them solicitors' letters about arrears, she revealed. FLAC previously criticised the Financial Regulator over its code of conduct on mortgage arrears.
It described the regulator's code as "deeply disappointing" and represented "even less protection for consumers than the draft code which the regulator prepared" in January.
The organisation said: "The original draft of this code was to provide for an accumulation of six months arrears before court proceedings could be issued.
The new and final version reduces that protection, such that a lender may start proceedings six months after any arrears at all, without requiring that the full six months must be owing."
It is estimated up to 30,000 people may now be in arrears on their mortgages, meaning they have failed to repay the mortgage for three months.
Permanent TSB has revealed 6,000 of its customers are in arrears of over three months or more. With Permanent TSB holding 20pc of the mortgage market, it is estimated the entire market has 30,000 mortgage holders in arrears.
More than 14,000 people are being helped to pay their mortgages by the Department of Social and Family Affairs.