The Metrolink commuter rail service plans to increase fares as early as July to help reduce a $13-million budget deficit largely caused by rising fuel and labor costs, railroad officials said Thursday.

If approved, the proposed increase of 5% to 9% will cover only part of the shortfall, making it necessary for Metrolink to seek additional subsidies from the five county transportation agencies that help fund the railroad.

“The current economic climate, including soaring fuel prices, requires tough decisions by transportation leaders to fund operations at a level that will continue to meet the region’s transportation needs,” said John Fenton, Metrolink’s chief executive officer. “Many transportation providers across the country and in the Southern California region are faced with the same challenges.”

Metrolink, which has 512 miles of track and an annual budget of about $194 million, has more than 40,000 boardings per weekday in six Southern California counties: Los Angeles, Orange, Riverside, San Bernardino, San Diego and Ventura.

The typical round-trip fare between downtown Los Angeles and Fullerton is now $15 and between Los Angeles and Riverside is $23. To go from Los Angeles to East Ventura costs $25.50, the same as a round trip between Los Angeles and Lancaster.

Officials estimate that $7.9 million of the budget shortfall has resulted from a 78% increase in fuel prices and a labor agreement that increased costs for the railroad’s contractors.

The rest of the deficit is the result of payouts for employee benefits that had not been budgeted for previously, rising maintenance costs caused by the addition of rail cars and costs related to the transfers of Metrolink riders to other transit systems.

Fenton said that without help from supporting transportation agencies, such as the Los Angeles County Metropolitan Transportation Authority, fares might have to be increased by 20% to eliminate the funding gap.

Metrolink will explain the proposed fare hike at a series of public workshops this month across its service area. They will culminate with a public hearing at the Metrolink board meeting May 30. Information about the workshops is available online at https://www.metrolinktrains.com.

dan.weikel@latimes.com