Correction: An earlier version of this story incorrectly said the first phase of the Silver Line project could be more than $250 million over budget. The first phase could be as much as $226 million over budget, according to current estimates. This version has been corrected.

Construction workers with Capital Rail Constructors lift a 2,000 pound girder into place on the Dulles extension of the Silver Line of the Metro on Tuesday, April 21, 2015 in Dulles, Virginia. (Pete Marovich/For The Washington Post)

The second phase of the Silver Line Metro extension is 13 months behind schedule and might not open for passenger service until 2020, project officials said Monday.

In addition, the rail line’s first phase, which opened in July, could be as much as $226 million over budget, according to current estimates. Officials said design modifications, along with work to finalize Phase 1, will add as much as $76 million to the project’s cost, putting its price tag at $2.98 billion. The first phase was $150 million over budget and six months late when passenger service began last summer.

Jack Potter, president of the Metropolitan Washington Airports Authority, which is overseeing construction of the $5.6 billion rail project, blamed the delays and overages in both phases on design changes. He said the six-month delay in finishing construction of the first phase also added to the cost for both portions.

Already, Potter said, there have been more than 150 design changes to the project’s second phase. Among the most significant: changes made to comply with new state and federal rules related to stormwater management.

“At the end of the day, we want to build something that is reliable and safe,” Potter said.

Since the Metro opened in 1976, six different lines have opened, totaling 117 miles with the opening of the Silver Line in 2014.

Monday’s announcement comes less than two weeks after the contractor told MWAA board members that the project was on schedule and that signs looked good for it to be completed in mid-2018. On Monday, the contractor, Bethesda-based Clark Construction, referred all questions about the delay to MWAA.

Potter offered no details on how much the 13-month delay would cost, saying MWAA is still negotiating with Capital Rail Constructors. He expressed confidence, however, that the additional expenses would be covered by a $551.5 million contingency fund.

Still dollars matter — particularly to users of the Dulles Toll Road who are paying for more than half of the Silver Line’s costs.

Potter said that the $76 million is an “upper range” estimate and that the actual overage could be less. Under the Silver Line funding agreement, MWAA and Fairfax and Loudoun counties would pay for about 25 percent, or $18.9 million of that cost. Toll road users would be responsible for the rest — roughly $57.1 million.

The cost increase is unlikely to lead raise tolls in the short-term because the project’s final price is unclear. Potter said it’s possible that the project could still come in under budget if Phase 2 ends up costing less than its projected $2.7 billion.

Phase 1 of the project includes five stations — four in Tysons and one in Reston. Phase 2 will have six stations, including one at Dulles International Airport, and will for the first time extend Metrorail into Loudoun County.

Loudoun spokesman Glen Barbour said the additional costs are unlikely to affect the county’s bottom line since it has set aside more than necessary to cover potential overages. And since the county is still negotiating to build parking garages at two Loudoun stations, officials will be able to adjust the schedule to accommodate the delay. Fairfax County also built in a contingency.

The Silver Line has been decades in the making — a project that has died, only to be revived numerous time. Sen. Timothy M. Kaine (D-Va.), who was governor during one of the most intense periods of negotiations, said recently it was the most difficult public project on which he had ever worked.

“While today’s news from MWAA is disappointing, nevertheless this project continues forward,” said Rep. Gerry Connolly (D-Va.), who was involved in the negotiations while chairman of the Fairfax County Board of Supervisors. “The construction delays on Phase 2 are primarily the result of a brutal winter and necessary safety-related design changes.

“While we all want to see the Silver Line completed as soon as possible, it’s more important to get it right and make safety our top priority,” Connolly said.

Although the rail line is being built by MWAA, it will be operated by Metro. Before Phase 1 opened, there were concerns that a pushed-back start date could cost Metro a substantial amount in lost fare revenue. Metro officials had no comment Monday on the Phase 2 delay.

Officials have known about issues related to stormwater management since September. At the time, project director Charles Stark said he did not expect the changes to have a major impact on completion of the rail line’s second phase. But the rule change did require contractors to redesign the entire 11.4-mile portion.

The first phase was built by Dulles Transit Partners, which was led by construction giant Bechtel. Potter said MWAA is close to reaching a financial agreement with Bechtel that will cover any outstanding work and settle remaining bills. However, Potter said that settlement will not be made public. In some instances, another contractor will be hired to complete some of the outstanding work that originally was Bechtel’s responsibility.

Potter said MWAA could have kept the project on schedule, but that officials concluded it would not be worth the significant additional costs. “We can afford to be a little patient,” Potter said.