The Ontario government will be cutting a subsidy that provides discounted fares for riders using GO Transit and Toronto’s transit system in the same trip, leaving the two agencies to come up with a way to keep the popular program running.

Regional transit agency Metrolinx, which runs GO trains and buses through the Greater Toronto and Hamilton region, said it hopes to work with the Toronto Transit Commission to sustain the program when the provincial funds run out next year.

The so-called Discounted Double Fare was created by the previous Liberal government in 2017 and offers riders using both systems, as well as the Union-Pearson Express to Toronto’s airport, a $1.50 discount for a single trip when using a Presto fare card.

The province paid $18.5 million a year to offset the cost of the discount for both transit agencies, but the current Progressive Conservatives say the funding was designed to be temporary. A three-year agreement on the subsidy is set to expire in March 2020.

Metrolinx CEO Phil Verster said in a June 18 letter to the TTC that a new cost-sharing agreement is needed for next year when the provincial funding ends.

“Metrolinx proposes a sustainable strategy for the continuation of this fare integration initiative, one that does not use a subsidy from the provincial government,” he wrote. “A new agreement and strategy is needed for next year and beyond.”

A spokesman for the Ministry of Transportation said Metrolinx’s proposed strategy — where it and the TTC share the cost of providing the discount — would allow both agencies to “mutually benefit from the revenue generated through increased ridership.”

The program has become so popular that it exceeded the provincial subsidy in 2018-2019 by $2.5 million and is on track to exceed it again, this time by $10 million, in the fall, Verster said in his letter to the TTC.

He said a new agreement to save the program is needed by October.

“Metrolinx intends to adopt the aforementioned discount to GO fares even if the City of Toronto and TTC decide not to match the transfer discount on the TTC fare,” he wrote.

TTC spokesman Stuart Green said Tuesday that nothing had been finalized but noted that Metrolinx had advised the agency of “potential changes to this popular program.”

“We have not yet responded as we need to understand the unanticipated cost pressures on our operating budget and report those to our board,” he said in a statement.

In a report to the agency’s board ahead of a meeting Wednesday, TTC CEO Rick Leary said a detailed cost-benefit analysis will be conducted before a decision is made in September.

“If the TTC continues with the program, there could be unanticipated budget pressures for the remainder of 2019 and all of 2020 due to the loss of the provincial subsidy,” Leary wrote.

NDP transit critic Jessica Bell criticized the government for cutting the subsidy, saying it should be promoting fare integration across transit systems in the region.

“Forcing commuters to dig into their pockets for an extra $1.50 per round-trip is going to hurt the monthly bottom-line for already-squeezed working people,” she said in a statement.