State Street has agreed to pay more than $64 million to end two federal probes into an alleged plot by two former executives to overcharge clients through secret commissions on trades worth billions of dollars.

The Boston financial services company (NYSE: STT) will pay a $32.3 million criminal penalty to the U.S. Department of Justice and a civil penalty in the same amount to the U.S. Securities and Exchange Commission.

State Street admitted that it added the commissions to trades performed on…