A former senior official at Anglo is suspected to have stolen more than €3m from a number of deposit accounts.
AIB has reported the matter to the Garda and has also informed the Central Bank.
In a statement this afternoon the bank said it has also begun an investigation and has insisted that customers will suffer no financial loss.
This issue came to light two weeks ago when a customer at Allied Irish Bank noticed an irregularity in a deposit account and contacted the bank.
AIB said this afternoon it has begun an investigation into whether any fraud occurred in what it says is a small number of transactions concerning certain discrete funds.
The funds in question are part of the €8.6 billion the bank acquired from the Anglo Irish Bank deposit book last February.
A former senior official at Anglo, who was based in Dublin, is suspected of moving large sums of money between accounts to cover the thefts, avoiding detection by ensuring that funds were available for accounts that matured.
It is believed the man at the centre of the allegations has since passed away.