Borrowers in some cases face rates doubling even though they took out tracker deals linked to the Bank of England base rate - which remains at a historic low of 0.5%.
Some of the 13,500 customers affected, many of whom took out loans with BOI subsidiary Bristol & West, face payments rising by hundreds of pounds a month. BOI has been contacting those affected - most of whom have a buy-to-let loan - about the changes, which take effect from Wednesday.
But consumer group Which? believes they are being treated unfairly, pointing out that some were sold a "lifetime tracker". It says customers should complain to the bank and if they are not happy with the response take the matter to the Financial Ombudsman.
Which? accuses BOI of justifying the changes on the basis of "clauses buried in the small print of mortgages" which were taken out before October 2004.
Which? executive director Richard Lloyd said this was "wholly unfair" and said BOI was "taking advantage of its customers by hiking rates at a time when the base rate is static", and added: "Customers should complain if they were led to believe they had bought a 'lifetime' mortgage and Bank of Ireland must deal with these complaints quickly and fairly."
A typical change will see a buy-to-let mortgage holder who is currently on a rate of 2.25% - made up of the base rate plus 1.75% - see it rise to 4.99%, representing the Bank rate plus 4.49%. For residential customers, changes will be introduced in two stages. They will pay the Bank rate plus 2.49%. On October 1, it goes up to Bank rate plus 3.99% - currently 4.49%.
One customer, Gary Smith, from Colchester, Essex, told the BBC he faced having to pay an extra £280 this month and a further £200 in October - after taking out a £200,000 mortgage with Bristol and West in 2004. He said: "It was sold and marketed as a tracker rate. I thought I had that margin for life. It's all very frustrating."
BOI blames the rise on increase funding costs and the need for banks to maintain greater levels of capital. It has set up a phone line for anyone worried about the impact of the changes.