THE MBTA IS ASSESSING KEOLIS Commuter Services financial penalties of about $608,000 a month, which is roughly 2.3 percent of the firm’s monthly fee of $26 million.

According to figures released by the T, 49 percent of the penalties Keolis paid over the first eight months of the current fiscal year were for trains failing to arrive on time, 27 percent were for trains lacking adequate seating and working toilets, 18 percent were for inadequate staff and service amenities, 3 percent were for failing to have enough locomotives ready for daily service, and the remaining 3 percent were for other issues.

Keolis was assessed $6.6 million in fines in fiscal 2015, $6.3 million in fiscal 2016, and is on track to cough up more than $7 million in fiscal 2017, which ends June 30. The fines are deducted from the T’s payments to the commuter rail operator, which will total nearly $315 million in fiscal 2017.

Keolis and T officials declined to discuss in any detail the way penalties are assessed. One official, who is generally familiar with the process, said fines are assessed if a required goal is not met but can be waived if there are circumstances beyond the commuter rail firm’s control as outlined in the contract. For example, the official said, a train that is late (defined as more than five minutes beyond the scheduled arrival time) is assessed a penalty. But the official said the penalty is not assessed if the delay was caused by something beyond the firm’s control, as outlined in the contract. Examples include a police or fire department hold on the train or a problem with a train crossing gate, the official said.

The official said the determination about whether a fine is required is usually made the same day as the incident or shortly thereafter.

David Scorey, Keolis’s general manager, indicated the company has no problem with the T’s penalty system. “Keolis is held to certain agreed-upon standards to ensure the safe, reliable, consistent commuter rail service that our passengers deserve,” he said in a statement. “We are very comfortable with the business process currently in place with the MBTA to determine appropriate penalties, assessed on a real-time basis, per the terms of our contract.”

Joe Pesaturo, the T’s spokesman, did confirm that no fines have been waived for Keolis’s failure to have 67 locomotives available every day, which is surprising since there have been indications in recent weeks that some locomotives have been out of service because of a defect in their turbochargers.

At a recent meeting of the T’s Fiscal and Management Control Board, officials said only 27 of the MBTA’s 40 relatively new locomotives were available as of March 31. The other 13 were undergoing some sort of maintenance. T and Keolis officials say the turbochargers on all of the new locomotives, manufactured by General Electric, are defective and will eventually have to be replaced.

According to T records, Keolis had only 64 locomotives available on March 31 and was assessed a fine of $3,000. Keolis faces a fine of $3,000 if it has 64 or fewer locomotives available, a $2,000 fine if it has 65 locomotives available, and a $1,000 fine if it has 66.

For the entire month of March, Keolis had the required number of 67 locomotives available on only four days. Keolis was assessed a total of $44,000 in fines for the month, including 11 days where the company was hit with the maximum $3,000 fine.

The locomotive requirement began July 1, 2016, in connection with a contract adjustment that gave Keolis $11 million more per year in return for adding nine locomotives and 12 coaches to the daily fleet. Keolis was also tasked with greater repair responsibilities for both locomotives and coaches. In the nine months since the penalty began, Keolis has been assessed a total of $192,000 in locomotive fines, or an average of $21,333 per month.

Keolis pays a $200 fine for each coach below the required level of 362. The coach fine began in December. The company paid $12,200 in fines in December, no fines in January and February, and $18,400 in fines during March. Keolis avoided fines for lacking the required number of coaches on only six days in March.

By far the biggest source of fines for Keolis is trains arriving late. In calendar year 2016, Keolis paid $2.7 million in fines related to on-time performance, or an average of $230,527 per month. The fines ticked upward in January and February this year, when fines totaled $356,284 and $381,434, respectively.

The second biggest source of fines is a category the T calls non-on-time-performance. Keolis was assessed $1.88 million in fines in that category in calendar year 2016, or about $156,721 a month. Most of those fines are for Keolis failing to have enough passenger seats available.