The Financial Industry Regulatory Authority has hit Raymond James & Associates and Raymond James Financial Services Inc. with an order to pay $1.69 million in restitution to more than 15,500 customers who were charged unfair commissions.

FINRA, a non-governmental regulator, also separately fined Raymond James & Associates $225,000 and Raymond James Financial Services $200,000. The fines were announced by FINRA on Thursday morning, and followed an investigation into commissions on securities transactions spanning from 2006 through 2010.

Both Raymond James businesses named in the case used automated commission schedules for equity transactions, but did not adequately decide on fair fees based on the kind of security or size of the transaction, FINRA said. The firm’s inflated schedules and rates resulted in excessive commissions for more than 27,000 transactions mostly involving low priced securities.

Altogether, more than 15,500 customers were charged more than $1.69 million in excess commissions from Jan. 1, 2006 through Oct. 31, 2010, according to FINRA.

“Broker-dealers must ensure that their automated systems set commission charges that are fair to investors,” Brad Bennett, FINRA executive vice president and chief of enforcement, said in a prepared statement.

Raymond James has also been ordered to change the automated commission schedules identified in the case to comply with regulatory rules.

In addition, Raymond James must also pay any additional overcharges on commissions that occurred from Nov. 1, 2010 until the new schedules are put in place.

In response to the investigation, Raymond James revised its automated commission schedules for the affected investments as of July 1, 2011, Raymond James spokesman Steve Hollister said via email on Thursday.

The affected trades represent less than 0.1% of the total equity trades made by the firm in the time frame examined by FINRA, according to Hollister. On average, each affected account lost about $110 over a five-year time frame.

"We are pleased to have resolved this matter with FINRA,” Hollister said.