KITTERY — Work to remove the USS Miami from active duty will be done at the Portsmouth Naval Shipyard, and workers there are 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 repairing the damage from an arson fire at the Kittery shipyard last year was “heart-wrenching.” The decision was announced late Tuesday.

Breckenridge said the work force won’t be affected because the Navy had decided previously to contract much of the repair work to Connecticut-based Electric Boat. One submarine maintenance project planned for Kittery will be shifted to Electric Boat to ease the impact of losing the USS Miami work, he said.

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

The sub will then 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 May 2012 fire, which was set by a shipyard worker, 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 directly affected by the fire, Breckenridge said Wednesday.

He said the amount of work far exceeded any repairs ever attempted by the Navy.

The forward half of the sub would have been essentially gutted and all of the equipment replaced, he said. That raised the cost estimate from the original $450 million, plus a $50 million contingency budget, to $700 million.

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

Breckenridge said the Navy’s budget is already 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 heat and smoke in the submarine’s cramped, unlit spaces.

Breckenridge said the effect of scrapping the USS Miami is compounded by the Navy’s need for submarines. Commanders’ requests for sub support outweigh the available number of vessels, he said.

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-Maine, said shipyard officials assured her Wednesday that they have a years-long backlog of work that will keep the work force 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, after lawmakers and President 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.

Edward D. Murphy can be contacted at 791-6465 or at:

emurphy@pressherald.com