(Reuters) - New York's Metropolitan Transportation Authority will need at least $20 billion from 2015 to 2019 to keep its system in good repair, but the mass transit operator has yet to figure out how to pay for these upgrades, a report said on Tuesday.

The MTA, the largest U.S. mass transit system, runs the city's buses, subways, commuter railroads and some major bridges and tunnels. Its capital needs are hitting customers in the wallet. Between 2007 and 2015 fares and tolls are set to have risen 35 percent, according to the report, issued by State Comptroller Thomas DiNapoli.

The estimate for the MTA's future maintenance does not include the cost of expansions, such as the second phase of the Second Avenue subway on Manhattan's East Side, which would extend the line from 63rd St. to 125th St., the report said.

The MTA's current capital plan, which runs from 2010 to 2014, totals $22 billion, an MTA spokesman said. This plan was cut from a proposed $28 billion due to a lack of funding, the report said.

In a statement, MTA Chairman Joseph Lhota said the comptroller's report recognized the MTA's significant financial hurdles, cost-cutting measures and "our ongoing efforts to address longer-term challenges, including identifying funding sources for our 2015-2019 Capital Program."

The authority is a major issuer in the $3.7 trillion municipal bond market. Its debt outstanding is expected to rise to $40 billion in 2016 from $31.8 billion at the end of 2012, the report said.

About 60 percent of the MTA's current capital plan is paid for with debt. If the authority relies on the same share of borrowing for its next capital plan, debt service could hit $4.4 billion by 2024, the report estimated. In 2012, debt service is expected to cost the MTA more than $2 billion.

Even with the biennial fare and toll increases that are planned, debt service as a percent of total revenue could rise to 19.8 percent by 2018 from 15.9 percent in 2011. Those are fairly high percentages. New York City, for example, has an informal policy of cutting its capital program when this ratio hits 15 percent, credit analysts say.

(Reporting by Joan Gralla; Editing by James Dalgleish)