The authority overseeing the $6 billion Metrorail extension to Loudoun County approved an agreement Wednesday for the financing of the second phase, a decision that moves the controversial project closer to construction.

The Metropolitan Washington Airports Authority (MWAA), which also operates Reagan National and Dulles International airports, also approved a “project labor agreement” to build the nearly 12 miles of rail line, which will run from Reston to Dulles and terminate at Ryan Road in Loudoun.

Financing for the Dulles rail extension, officially known as the Silver Line, has been debated for years.

The first phase is under construction and is expected to open to riders in December 2013, although concerns have been raised recently that it could be as much as $150 million over budget.

One of the biggest disputes in building the second phase was whether a rail station at Dulles should be aboveground or underground and closer to the main terminal, at a greater cost.

For the past four months, stakeholders — including MWAA officials, representatives from Loudoun and Fairfax counties and Metro, which will operate and maintain the Silver Line — have met with U.S. Transportation Secretary Ray LaHood to reach an agreement. Last week, the group agreed on a deal that codified how the partners would pay for the $2.8 billion second leg. Each stakeholder’s respective board has to sign off on the deal. Loudoun approved it Tuesday night, and Fairfax is expected to approve it in December.

As part of the deal, the two counties and the airports authority are expected to receive federal loan assistance to finance their portion on the project. MWAA officials said they expect to receive about $250 million in federal loans.

The two counties are expected to seek public-private partnerships to build parking garages and the Route 28 station in Fairfax. Virginia agreed to put $150 million into the deal. They are expected to put out a request for bids in the spring.

But concern remains that Dulles Toll Road users, whose payments go in large part to help pay for the rail project, will see much higher rates.

Bob Brown, chairman of the board’s finance committee, said he worries that if the counties can’t come up with their contributions, responsibility will revert to MWAA and ultimately be passed on to drivers.

“We have gotten an agreement together, but we haven’t really made any progress toward moving tolls,” he said.

Tom Davis, board vice chairman, noted that the second phase of the Dulles rail line still has “a lot of land mines ahead of us.”

“The future is going to call for higher tolls, higher subsidies,” he said. “This is not for free, but this is in Virginia and the region’s future.”

After the meeting, board Chairman Charles Snelling and Mame Reiley, who chairs the Dulles rail committee, would not say whether they would consider imposing a toll on the access road to the airport to help pay for the new rail line.

“We will look at all options,” Reiley said. “We do believe in shared sacrifice.”

The labor deal the board approved Wednesday will include rates, overtime, work hours, training and define which jobs can be done by union versus non-union workers.

Some Virginia lawmakers had expressed concern that such an agreement would be in violation of the state’s right to work laws. But airports authority board members said the agreement abides by state law.

The airports authority board has come under increased scrutiny for how it operates and oversees the Dulles rail project. Virginia lawmakers asked the U.S. Department of Transportation’s Inspector General to do an audit of the quasi-public entity. The review is due this spring.

Rep. Frank R. Wolf (R-Va.) also has introduced legislation to change the structure of the MWAA board. He’s proposed increasing it from 13 to 17 members. It would include adding two members from Virginia and one each from the District and Maryland. Board members could also be removed “for cause.”

The House is expected to vote Thursday on the legislation, which is part of the Department of Transportation appropriations bill. The Senate is expected to vote Friday.

Reiley called Wolf’s legislation a “form of intimidation.”

“It’s simply expanding [the size of the board],” she said. “It doesn’t make sense to me.”