Workers are set to return to the building, Vice Adm. William Hunter Hilarides, the commander of the Naval Seas Systems Command, said.
"There will be some people who won't go back," he told Stars and Stripes. "I don't think there will be many. But there are some people who have already made it clear."
The employees who decide not to return to the building will work in another building or location.
The structure underwent a $6.4 million contract for restoration in late September, but officials said they were not sure about the building's future use at the time.
The work came after Aaron Alexis, a former Navy Reservist who had access to the building, fired at employees with a shotgun.
The 34-year-old was killed after exchanging gunfire with police.
Hilarides said 2,700 employees worked in the building, and many of them are expected to return in the next few weeks.