Thursday night’s fire on a nuclear-powered submarine at the Portsmouth Naval Shipyard could have been a disaster. It still might be.

Thanks to the teams of courageous firefighters who donned air packs and fought through toxic fumes to control the stubborn fire, the USS Miami may be salvaged. But that is not a certainty. The Los Angeles-class submarine may have been damaged beyond repair. That would be nearly a billion-dollar loss for the Navy and a tremendous blow to the shipyard.

In the short term, jobs might be endangered if the Miami’s 20-month overhaul is aborted. But if Portsmouth’s reputation for efficiency is tarnished, its entire future becomes uncertain.

Paul O’Connor, the president of the shipyard workers’ union, called the fire “an absolute tragedy ... the most significant event in my 36-year career.” That suggests O’Connor considers the fire’s impact even more important than the 2005 battle in which Portsmouth narrowly escaped the Base Closure and Realignment Commission’s axe.

That risk remains. The Pentagon still wants to eliminate bases. Even though Congress does not, the unprecedented budget crunch looming at the end of 2012 could give the Department of Defense powerful leverage.

The base has solid political support in New England and both of New Hampshire’s senators are outspoken opponents of base closures. Kelly Ayotte told her Armed Services readiness and management subcommittee recently that since the country is “still paying for previous BRAC rounds from decades ago, it makes no sense to spend tens of billions on a new base closure process. ... Savings can certainly be found within the Pentagon’s budget.” Jeanne Shaheen reaffirmed her opposition to base closures on Thursday, arguing that “the last time we went through this process, it ended up costing us 50 percent more than we were told and it achieved significantly less savings than we expected.”

But as long as the cause of the fire is undetermined, expect powerful advocates of other endangered shipyards to malign Portsmouth’s competence and efficiency. That is why Rear Admiral Rick Breckenridge’s immediate public promise of a thorough investigation is good news.

If the shipyard is not at fault, that finding needs to be publicized as soon as possible. If Portsmouth shares the blame, the shipyard must quickly make any changes necessary. This is not new. It did so nearly a half-century ago after a truly tragic disaster. After its USS Thresher was lost during sea trials on April 10, 1963, federal investigators criticized the yard’s procedures. Portsmouth responded by fixing the flaws and rebuilding its image as one of the nation’s essential defense assets. If necessary, expect its skilled workforce to do so once again.