Public Safety Commissioner Kevin Burke said the state Department of Correction violated its moral and ethical obligations.
"None of this is acceptable," Burke said. "There is no reason for any kind of error given the system and the numbers of lawyers who examine these cases."
According to a report in the Boston Sunday Globe, the prisons department in some cases failed to modify some sentences for time spent on parole. The department in some cases relied on an inadequate computer system that tracks time served and good behavior credits, or simply botched the math.
One man, Rommel Jones, was released from prison in July 2006, four years after his sentence was done.
Jones, 40, diagnosed with schizophrenia in 1997, was unaware that his sentence was up in 2002, when he was denied parole.
The Department of Correction initially told the Globe that Jones' error was a bookkeeping anomaly. It later acknowledged it to be a serious error.
However, the department never told Jones of the mistake, even after releasing him last July.
Commissioner Kathleen Dennehy, who is leaving her post next month, said Jones' mental illness would have made it difficult for him to understand what happened.
"I think we could have been criticized for explaining this to someone ... with the history of mental illness that this individual has," she said.
Burke said in a story in Monday's editions that Dennehy's departure presents a chance to review the system.
State Senator Jarrett Barrios said the mistakes warrant a legislative hearing.
The other 13 inmates held too long also were not alerted until letters were mailed to them Friday after the Globe's inquiries.
Prison officials said they have reviewed their records to make sure no one else is affected.