A top federal transportation official has raised concerns about what he says were unauthorized changes made to safety systems for Metro’s new Silver Line.

Dealing with the changes and with faulty testing of the safety systems could delay the December opening of the $5.6 billion rail extension, officials said.

Federal Transit Administrator Peter Rogoff, in a letter to local officials, said he was troubled by a contractor’s failure to obtain approval for the changes to what is known as the automatic train control system.

The controls serve the same function as those that failed in the fatal 2009 Red Line crash, and the contractor is the same company that manufactured the Red Line controls.

In his letter, obtained by The Washington Post, Rogoff said the contractor, Alstom Signaling, “unilaterally made various design changes to the [automatic train control system] without prior approval” from Metro or the Metropolitan Washington Airports Authority.

The letter, dated May 17, was sent to Jack Potter, president and chief executive of the airports authority, which is overseeing construction of the rail extension to Dulles.

Rogoff wrote that the changes were “alarming,” given that the National Transportation Safety Board found that a failure of track circuit equipment built by what is now Alstom Signaling was one of the causes of the Red Line crash, which killed nine people and injured dozens more. Alstom Signaling, a subsidiary of the French infrastructure giant Alstom, was known as General Railway Signal Co. before it was acquired in 1998.

“The scrutiny of the ATC system following the accident,” Rogoff wrote “should have strengthened GRS/Alstom’s practices — not weakened them.”

The first phase of Metro’s Silver Line, one of the largest public transportation projects in the country, is under construction and is expected to be ready for passengers late this year or early next year.

Dulles Transit Partners, led by the international construction and engineering giant Bechtel, is building the first leg of the rail extension, an 11-mile stretch from East Falls Church to Reston.

The situation that prompted Rogoff’s letter arose because of a shortage of electronic control boards that help transmit signals along the rail line to trains, according to three officials with oversight roles. In the course of testing, Alstom workers allegedly moved some control boards from one monitoring station to another, said the officials, who spoke on the condition of anonymity because they were not authorized to discuss the matter publicly.

As a result, one of the officials said, the workers “were checking the same set of boards over and over again.”

When oversight personnel began examining the testing problems, they found that Alstom also had made design changes without approval.

The problems were detected by an oversight team that includes Metro and MWAA employees, according to Pat Nowakowski, executive director of the Silver Line project for the airports authority.

Potter, the MWAA president, said the oversight worked the way it was intended to.

“We have people out there who observed things and said it was done inappropriately and called them on it,” Potter said Thursday. “Any testing they did is going to be redone.”

“All changes are going to be documented, and the system is going to be thoroughly tested before it is accepted,” Potter said. “We are not going to turn over an unsafe rail project to [Metro.]”

Dan Stessel, a spokesman for Metro, referred questions to MWAA.

Adam Pratt, a spokesman for Alstom, wrote in an e-mail Thursday, “We respectfully decline the opportunity to comment.”

Leslie Pereira, a spokeswoman for Bechtel, said in an e-mail that Alstom had made changes without approval. Bechtel has meet with Alstom senior management, she said, to “strongly reinforce the need to follow procedures.”

The problems underscore complications related to Metro’s relying on other entities to build its infrastructure. In the case of the Silver Line, MWAA, with revenue from the Dulles Toll Road, was tapped to finance construction of the rail line, which eventually is supposed to run to Dulles International Airport and Loudoun County.

Meanwhile, the troubled Silver Spring Transit Center is being built by contractors for Montgomery County, and Metro has said it will not take ownership of the transit hub until structural problems are resolved.

In both cases, Metro has a limited role in the construction phase.

The Silver Line is the first Metrorail line not built by the transit agency, which opened the rail system in the 1970s.

Nowakowski said additional testing could prevent the Silver Line’s being turned over to Metro by the September deadline.

Metro has said it will need 90 days to test the new rail line before it starts carrying passengers in late December or early January. It is unclear whether the changes will add to the cost of the project, which is already over budget.

“We’re in no way shape or form going to allow safety to be compromised,” Nowakowski said.

“We will do this the right, proper way so that everybody can be confident that the traveling public will be safe riding on this line and the system will work reliably.”

Jennifer Jenkins contributed to this report.