CSX wants to add a second track and have the tunnel deep enough to accommodate double-stacked container freight trains. (Katherine Frey/The Washington Post)

Before the federal environmental process was completed on a proposal to rebuild a tunnel in Southeast Washington, the D.C. Department of Transportation had given the project’s applicant clearance to take over the road it needs for the construction, irking some opponents of the project.

DDOT issued an occupancy permit nearly two years ago guaranteeing CSX Transportation the right-of-way at Virginia Avenue SE, and adjacent roads, so the company could reconstruct the 110-year-old old tunnel that is underneath, according to documents in the final environmental statement released last week.

Some residents who live near the tunnel say they are baffled by DDOT’s negotiations with CSX while the proposal was still going through a mandatory federal review process.

“We hope that the District government has not thrown us under the freight train,” said Helen Douglas, a member of DCSafeRail, a coalition of residents fighting the project.

“At best, this indicates that the District government is failing to uphold basic principles of good government, including transparency and accountability,” Douglas said.  “At worst, it suggests that the environmental study is a farce because it rubber-stamps the CSX open-trench proposal.”

CSX plans to convert the single-track tunnel into two tracks and rebuild it to allow for double-stacked freight cars.  The company says the tunnel, which runs underneath Virginia Avenue SE, from Second to 11th streets, has structural problems that need to be fixed to avoid failure.

Last week the Federal Highway Administration and DDOT issued a final environmental impact statement backing a $170 million construction alternative for the project, moving the project a step closer to construction. The federal agency is expected to release a final decision on the project next month.  If that decision supports construction, CSX will have final clearance to move forward with the project.

Some residents were under the impression that CSX would go through the local  permitting process after the completion of the environmental review, and not concurrently.

Documents in the final environmental impact statement show that DDOT first issued the occupancy permit in December 2012 and has committed to deliver construction permits to the company promptly after Federal Highway Administration issues the record of decision. The office of the city administrator also has also agreed to expedite any other permits and approvals for the project.

DDOT spokesman Reggie Sanders said in an e-mail that the permit relative to Virginia Avenue SE and adjacent streets “will have no force or effect until a build alternative is approved via Record of Decision.”  Other requests for comment regarding the city’s commitment to the project have not been answered.

The city also has asked CSX to extend the tunnel to 12th Street SE.

DCSafeRail is asking Mayor Vincent C. Gray (D) to withdraw the permits approved  before the environmental impact statement was completed, and conduct a study of other alternatives to project. The group said it also plans to seek City Council hearings on the project.