KITTERY — Work to remove the USS Miami from active duty will be done at the Portsmouth Naval Shipyard, whose workforce is not expected to be affected by the Navy’s decision to scrap the submarine, at least in the short term, a Navy official said Wednesday.

Speaking on a conference call, Rear Adm. Rick Breckenridge, the Navy’s director of undersea warfare, said the decision to forgo repairs instead of fixing the damage caused by a fire set by a shipyard worker last year was “heart-wrenching.”

However, he said the workforce at the shipyard in Kittery won’t be affected because the Navy had decided previously to contract much of the repair work to Connecticut-based Electric Boat.

Breckenridge said one submarine maintenance project that was to be done in Kittery will be shifted to Electric Boat to ease the effect of its loss of the work on the USS Miami.

Shipyard workers will remove equipment that hasn’t been taken out of the Los Angeles-class submarine already, including fuel for the nuclear reactor. That work will cost about $54 million and take about 18 months, Breckenridge said.

The submarine then will be taken to Washington state to be cut into sections for scrap. The reactor will be sent to Hanford, Wash., for deactivation.

Immediately after the fire in May 2012, Navy officials said they would repair the USS Miami and return it to duty. That was before the discovery of cracking in pipes and other damage in areas that weren’t affected by the fire directly, Breckenridge said Wednesday.

He said the amount of work that would have been needed was four times the level of repair the Navy ever had attempted.

The Navy announced its decision late Tuesday.

Breckenridge said the forward half of the submarine essentially would have been gutted and all the equipment there would have been replaced. That pushed the cost estimate up from the original $450 million, plus a $50 million contingency budget, to $700 million.

Los Angeles-class submarines cost about $900 million to build, in 1990 dollars, which is when the Miami was commissioned.

Breckenridge said the Navy’s budget already is stretched because of federal spending cuts, and shifting more money to the USS Miami would have largely eliminated funds for other maintenance projects. “We just don’t have the money,” he said. “It was a very, very challenging decision. It was heart-wrenching.”

Casey James Fury, the shipyard worker who set the fire, was sentenced in March to 17 years in prison and ordered to pay restitution of $400 million. More than 100 local and shipyard firefighters battled the blaze for hours, hampered by the submarine’s cramped, smoke-filled, hot and unlit spaces.

Breckenridge said the effect of the scrapping of the USS Miami is compounded by the Navy’s need for submarines. He said commanders’ requests for submarine support outweigh the available number of vessels.

The USS Miami was expected to have a service life of at least 10 more years, meaning five deployments of six months or more; but budget problems left the Navy with no choice, Breckenridge said.

U.S. Rep. Chellie Pingree, D-1st District, said shipyard officials assured her Wednesday that they have a yearslong backlog of work that will keep the workforce stable.

Pingree said she was upset with the Navy’s decision; but she blamed Congress, which passed the legislation that created the automatic spending cuts in March, when lawmakers and President Barack Obama couldn’t agree on a new budget deal. Pingree voted against that legislation.

“It’s hard to imagine the budget constraints we have them operating under,” she said. “We’ve got to change that.”

Pingree is married to S. Donald Sussman, majority share owner of the Portland Press Herald.