KITTERY — The arson-damaged USS Miami will be deactivated at Portsmouth Naval Shipyard and extra repair work will be steered to Connecticut-based Electric Boat, minimizing the effect on workers at both shipyards, the Navy’s director of undersea warfare said Wednesday.

Rear Adm. Rick Breckenridge laid out details of the submarine’s deactivation in a conference call with reporters a day after the Navy announced plans to scrap instead of repair the Los Angeles-class attack submarine.

The Navy abandoned the repair because the estimated cost jumped from $450 million to $700 million during a time of budget cuts.

“We recognized from the start that repairs to Miami presented a significant technical challenge. The type of damage was unlike anything we’d seen in recent memory, meaning the effort contained plenty of unknowns,” Breckenridge wrote Wednesday on the Navy website.

The nuclear-powered submarine based in Groton, Conn., was severely damaged by a fire that was set by a shipyard worker in May 2012 while the sub was in dry dock during a 20-month overhaul in Kittery.

It took 100 workers about 12 hours to douse the fire, which damaged forward compartments including living quarters, a command and control center and the torpedo room. Seven people were hurt.

There had been considerable speculation about whether it made sense to repair the sub because the extensive damage.

Loren Thompson, a defense analyst at the Lexington Institute, said shortly after the fire that he’d be surprised if the Navy elected to repair the sub because it was already 22 years old at the time.

“The Navy’s original decision to fix the sub was really quite questionable in light of threats and budget circumstances. So I think they’ve made the right call here,” Thompson said Wednesday from Virginia.

To mitigate impact on shipyard workers, Portsmouth Naval Shipyard workers will be tasked with stripping the sub and removing the reactor before the Miami is shipped to Washington state to be cut up for scrap, the Navy said.

The Navy also will aim to find extra work for Electric Boat, which built the submarine and was playing a major role in the repairs. That means another submarine, likely the USS Providence, will be brought to Electric Boat for maintenance, the Navy said.

U.S. Sen. Susan Collins of Maine said Wednesday she received further assurances from the chief of naval operations that the Navy would not cut back on a scheduled submarine overhaul next year in Kittery.

Breckenridge said the repair would’ve been four times greater than any previous submarine repair due to damage.

Extra repairs to cracked pipes drove up the price and sequestration raised questions about the availability of Portsmouth Naval Shipyard workers to provide lead yard services for Electric Boat production workers, he said.

“In times of prosperity with more flexible defense spending, sufficient resources would be available for our industrial base partners to rise and tackle this formidable challenge. However, sequestration pressures remove the needed foundation of stability to support an endeavor of this magnitude,” he said.