WASHINGTON — The Senate passed legislation today that preserves a key federal funding source for the Downeaster train service between Portland and Boston.

A two-year transportation bill approved 74-22 allows Maine to keep relying on money from a federal program that supplies the Downeaster with as much as $6 million a year, more than a third of its annual operating budget of about $15.1 million.

An initial version of the bill eliminated Maine’s ability to use money from the federal Congestion Mitigation and Air Quality program to help run the Downeaster, which serves about a half-million riders a year.

But Sen. Olympia Snowe, R-Maine, got a provision included in the bill that keeps the funding source in place. Snowe and Sen. Susan Collins, R-Maine, who backed the Downeaster funding provision, both voted yes on the overall bill.

The Northern New England Passenger Rail Authority, which manages the Downeaster on behalf of Maine, brings in about $8 million a year from sources such as ticket sales and food concessions, leaving about a $7.1 million shortfall. The rail authority pays about $12 million a year to Amtrak to operate the Downeaster.

Depending on the year, the federal money is used to cover $5 million to $6 million of that shortfall. The rest comes from revenue raised by a state-imposed car rental sales tax.

In a five-year transportation bill passed in 2005, Maine won an exemption that allowed it to keep using the money for the life of the transportation bill.

Congress has not passed a new transportation bill since then, and the exemption has been retained in a series of temporary measures. The original version of this Senate transportation bill omitted the exemption.

When the Downeaster service began in 2001, it was allowed to use the air quality program money temporarily, on the theory that the train was keeping cars off the road and improving air quality.

A pending transportation bill in the House still does not contain the Downeaster funding exemption, but the Senate bill is considered more likely to attract bipartisan support.

It’s also possible the House won’t approve any bill before the current temporary transportation measure expires March 31. That likely would mean Congress approves another temporary transportation bill – which would keep the Downeaster funding source in place at least for the time being.

The Senate’s $109 billion transportation bill also includes a slight increase in the amount of federal road repair money Maine receives. Under the bill, Maine would get nearly $195 million this year and about $198 million in 2013, a hike over its 2011 allocation of $191.6 million, according to the office of Snowe, a member of two committees that helped craft the Senate bill — the finance committee and the commerce, science and transportation committee.

The entire Maine congressional delegation backed preserving the Downeaster’s federal funding source. Maine lawmakers have noted that Congress recently approved spending $38 million to extend Downeaster service north to Brunswick, and millions of dollars more to improve rail lines in Massachusetts.

Snowe won several other amendments to the transportation bill, including a provision that streamlines the process for veterans who already have the property military training to get a commercial driver’s license.

MaineToday Media Washington Bureau Chief Jonathan Riskind can be contacted at 791-6280 or at: jriskind@mainetoday.com Twitter: Twitter.com/MaineTodayDC