KITTERY – The nation’s oldest federal shipyard, targeted for closure by the Pentagon, received bittersweet recognition of its work Thursday: a commendation from the Navy acknowledging the shipyard’s performance.

The Meritorious Unit Commendation was given to the Portsmouth Naval Shipyard for its “phenomenal record” of refueling and overhauling nuclear submarines ahead of schedule, the Navy said.

Then-Navy Secretary Gordon England awarded the commendation on May 12, one day before the Pentagon released its list of recommended base closures.

The commendation was presented formally to the yard at a ceremony Thursday, just days before a critical hearing in front of an independent panel that will help decide the shipyard’s fate. New England lawmakers will make their case before the Base Closure and Realignment Commission on Wednesday in Boston.

“In the back of our heads we get this incredible award and we wonder, ‘Why are we on this list?'” said Paul O’Connor, president of the shipyard’s Metal Trades Council, a labor union group with 2,300 members.

Officials chose to overlook that detail Thursday.

“The Navy and the country need you to keep doing what you’re doing,” said Rear Adm. Anthony Lengerich, acting commander of the Naval Sea Systems Command. “And I mean by that your professionalism, your reputation, your innovation and your enthusiasm for giving to the taxpayer the value they well deserve.”

Hundreds of workers were in the audience and some shouted “We’re number one!” at the end of the ceremony. The commendation is for service between Sept. 11, 2001, and Aug. 30, 2004.

Speaking to reporters afterward, Lengerich sidestepped a question about whether Portsmouth deserved to be on the Pentagon’s list.

“That’s not a question for me to answer,” he said. “We’re talking about a celebration for these folks, for what they’ve done, and the performance they’ve had and we’re happy to celebrate that.”

The Pentagon says it no longer needs four bases where ships are repaired and refueled. It says shuttering Portsmouth will save $21 million initially, then $129 million annually by shifting work to yards at Norfolk, Va., Pearl Harbor, Hawaii, and Bremerton, Wash.

Critics of closing Portsmouth question the Pentagon’s projected savings. They argue that the base fixes and overhauls submarines faster than the other shipyards, saving the military tens of millions of dollars per vessel.

Instituted in 1967, the Meritorious Unit Commendation is only given to “high performing units,” said Pat Dolan, deputy director of public affairs at Naval Sea Systems Command.