A review of the Suffolk Department of Fire and Rescue’s pay practices found the fire department has been shorting firefighters on their overtime pay for at least three years, the city said Wednesday.

The problem was discovered during a review initiated by Chief Cedric Scott. Fire suppression personnel were paid about $1 less for each overtime hour than they should have been, said Jeff Gray of the city’s human resources department.

“It’s unclear when that actually occurred,” Scott said of when the discrepancy started. “The calculation was discovered because of the review.”

Checks were distributed to all employees, past and present, who were affected within the last three years. City Chief of Staff Debbie George said the city is required to give back pay for only three years.

“That is what the city is required to do, and that is what the city has done,” she said.

Employees had to hand-tabulate the totals owed to each firefighter, she added, which took several weeks. Changes such as promotions were also taken into consideration for each individual, she said.

Scott met with personnel Monday, Tuesday and Wednesday this week to explain the situation, he said.

The revelation that firefighters have been shortchanged for years — and won’t get some of it back — comes about three months after the city accidentally overpaid some fire and rescue personnel and then took the difference from their next check.

That happened in December, when the fire department submitted an incorrect file to payroll, George said. When the mistake was discovered, direct deposit information had already gone to the banks, and there was no way to reverse it without affecting everybody’s paychecks in every city department.

Therefore, fire and rescue employees were told before they were paid that some of the money wasn’t theirs to keep. The difference was deducted from their next check, George said.

“No one received less than they should have,” she said. “Most received more, but with the understanding it was going to be negated in the next paycheck. We worked very hard to get that corrected and make sure everyone was very clear on how to get it corrected and make sure there were no surprises for anyone.”

George also said pay stubs will start showing a breakdown of hours worked starting with the March 30 paychecks.