BOSTON — Keolis, the international company that won a tough competition to run commuter trains out of Boston, may have second thoughts about its contract with the Massachusetts Bay Transportation Authority. According to a report by State House News Service, Keolis lost $29.3 million over the first year of its long-term contract, requiring its French parent company to subsidize its Massachusetts operations.

According to Massachusetts Transportation Secretary Stephanie Pollack, Keolis Commuter Services likely failed to fully account for the cost of providing service to the region.

Keolis won the contract in January 2014 over Massachusetts Bay Commuter Railroad. The bid would pay Keolis $2.69 billion for the first eight years with an option to extend an additional four years for a total cost not to exceed $4.26 billion.

A Keolis representative said in a statement that fixing MBTA’s issues had taken longer and proved more costly than the railroad operator expected and that Keolis is looking for ways operate “more efficiently.”