MBTA OFFICIALS KNOW that commuter rail riders hate late trains. They also get an earful about conductors who fail to collect fares and the passengers who evade paying them.

So the transit system plans to use one problem to solve the other.

MBTA interim general manager Frank DePaola announced Tuesday that Keolis, the MBTA commuter rail operator, will hire fare agents to collect fares and to assist conductors to get people on trains, which will free up conductors to handle other issues like fare evaders.

The MBTA will use a portion of $7.5 million in on-time performance penalties that Keolis paid the transit agency from October 2014 through June to hire about 30 fare collection agents. The operator had a four-month grace period on penalties when it took over operations last July, and no fines were assessed during that period.

The MBTA and Keolis are currently negotiating an agreement to hire fare agents with the United Transportation Union, a Keolis labor group. New employees will undergo about two weeks of training through an apprentice program that will put them on a path to conductor positions, according to DePaola, who described the plan during the first meeting of the MBTA Fiscal and Management Control Board. An expected increase in fare revenues will help pay for the agents going forward.

Penalty dollars will also be used to hire passenger information staff to provide service updates online and at individual stations. “We’re hoping that the customer information people can keep up with what’s happening in the control room, so that we can push those alerts out on a more timely basis,” said DePaola.

Commuter rail riders should also notice that the MBTA has stepped up its game in the cleanliness department, as the T is using the penalty monies to buy equipment to steam clean commuter rail coaches during overnight layovers.

Keolis paid millions in penalties because it trigged provisions of its contract that call for fines if trains fail to arrive within five minutes of scheduled arrival time; 50 percent of possible penalties are related to on-time performance. The rail operator pays $500 for a rush-hour train that is five to 10 minutes late; $2,000 for heating, ventilating, or air conditioning that does not work; and $5,000 for a rush-hour train that gets cancelled.

“Keolis has good days and bad days and good weeks and bad weeks,” said Transportation Secretary Stephanie Pollack after the meeting. “What has been frustrating is the lack of consistent progress toward consistently meeting on-time performance metrics.”

Keolis’s on-time performance remains spotty, especially during rush hours. But the operator is within the parameters set by its predecessors, DePaola said. Amtrak operated commuter rail for the MBTA from 1978 to 2003 and Massachusetts Bay Commuter Railroad ran the trains from 2003 to 2013. MBCR faced some of the same issues that have plagued Keolis. DePaola also noted that if winter performance was taken out of the equation, Keolis performed as well if not “a little bit better than the average” of MBCR.

Keolis took over the MBTA’s commuter rail operations in July 2014. On-time performance ranged from a high of 90 percent in August 2014 and a low of 86 percent in January 2015. Performance plummeted during the worst of the winter weather in February, when only 39 percent of trains were on time.

“The data says that from an on-time performance standard [no previous operator] has ever done better than the high eighties,” said Pollack. “That said, it’s really hard to run a commuter rail system consistently on 90 or 92 percent on-time performance.”

Keolis has also suffered from management issues. Staffing shortages have triggered penalties as its contract with the MBTA specifies that Keolis must provide one conductor for every 300 passengers.

“The contract with Keolis was structured such that we penalized them for not meeting requirements,” said DePaola. MBCR “was rewarded for exceeding requirements; in this case we flipped the paradigm to expect top performance.”

“Keolis does not get that revenue and it affects Keolis’s bottom line,” said Pollack. “Hopefully, that is an incentive to get their performance better so that they are not fined.”

Although on-time performance is slowly rebounding, ridership has yet to bounce back. Ridership dipped below 2.7 million passenger rides in May after rebounding to 2.9 million in April. When Keolis took over the contract last July, ridership had reached 3.1 million. However, DePaola said ridership numbers “were suspect” because of the unreliability of commuter rail passenger counts. Nevertheless, monthly commuter rail pass sales remain healthy. The MBTA sold 46,000 commuter rail passes in May 2015 compared to about 42,000 the previous May, which DePaola attributed in part to corporate pass programs. Some companies allow commuters to buy passes on a pre-tax basis or subsidize some portion of the cost.