Federal investigators have rejected Bath Iron Works’ claim that the Navy failed to follow its own protocol when it chose another shipbuilder as the lead designer for the new DD-X battleship.

In a report that has not been released publicly, the General Accounting Office upheld the Navy’s decision in April to make Ingalls Shipbuilding Inc. the lead designer for the new family of warships.

BIW and its parent company, General Dynamics Corp., filed a 72-page protest that called the Navy’s decision “clearly flawed.” The protest was based on the way the Navy graded the proposals and a dispute over the use of an existing ship’s hull to test radar.

BIW will still work on the project. Plans call for the shipbuilding to be split between Maine and the Ingalls shipyard in Pascagoula, Miss.

GAO, which reviews bid protests involving federal agencies, has not released the 26-page report. But GAO, General Dynamics and Navy officials confirmed the decision Tuesday.

An edited version of the report will be released after the Navy and both companies review it, possibly in about two weeks, a GAO official said.

Much of the review was conducted in secret because it involved national defense and confidential corporate information.

General Dynamics spokesman Kendell Pease said the company appreciated the chance to have its protest heard, adding that the acquisition process would benefit from it.

“Now is the time to move ahead,” Pease said. “We look forward to working with the Navy and Northrop Grumman on this very important project.”

General Dynamics could ask GAO to overturn its decision or challenge it in the Court of Federal Claims, but GAO decisions in bid protests are rarely overruled, according to Daniel Gordon, managing associate general counsel and head of the bid protest unit.

Pease declined comment on a possible appeal because the company had yet to review the report fully.

To overturn the Navy’s decision, BIW had to prove that the Navy violated procurement rules and hurt BIW’s chances by doing so.

BIW officials protested that Ingalls planned to use a DD-963 Spruance hull to develop the ship’s new radar when they were told they couldn’t pursue that strategy.

The protest also said there were disparities in grading the two proposals between different levels of Navy officials.

Without discussing details of the complaint, Navy officials have said major advantages of the Ingalls proposal included stern launching for special-operations rafts and a pair of helicopter landing pads on the deck.

BIW and Ingalls will jointly build an undetermined number of the new destroyer, which will have a special electric engine, more computerization and a gun that can fire accurately 100 miles inland.

In the design stage, the shipyards will divide 38 percent of the $2.9 billion contract, with electronics and weapons contractors sharing the rest.