A senior official in Defence Minister Peter MacKay's office would not say how many people have moved, but that it has been conducted as a precaution.
The Defence Department, in a statement, downplayed the event.
"As part of a normal and prudent business contingency plan, personnel belonging to elements of HMCS Trinity have been relocated to 12 Wing Shearwater for an undetermined time period as a security precaution," said the email note.
The highly-secure Trinity establishment, located behind razor wire at Canadian Forces Base Stadacona in Halifax, has been home to the navy's information gathering effort for years. It was the office that analysed eavesdropping on Soviet submarines during the Cold War and has since morphed into what the military calls an all-source fusion centre, where data from a variety of military and civilian agencies, including police and border services, is pulled together.
Sub-Lt. Jeffery Delisle, who was assigned to the section last August, has been charged with two counts of breaching the Security of Information Act by allegedly passing secrets to a foreign entity.
National Defence would not say what elements of the office have been shifted to the Dartmouth, N.S. air base.
A former navy commander called the timing of the move "odd" but refused to speculate on whether it meant some of the base's networks had been compromised — of if it was an attempt to contain the damage.
"It's an information-sharing piece. Obviously, there are some secure networks and stuff you have to put in, but it's not much more than that. Everything is pretty portable," said retired vice-admiral Bruce McLean.
He said the intelligence centre has expanded over the last few years and could very well be outgrowing its old location.
Meanwhile, the lawyer for a Canadian navy intelligence officer accused of passing information to a foreign entity withdrew from the case Monday.
Cameron MacKeen told a brief proceeding in Halifax provincial court that he could not longer continue representing Delisle, a court official said.
Reached by phone later in the day, MacKeen declined comment.
Delisle was expected to return to court Wednesday, but a spokesman for the federal Prosecution Service said his next court appearance is now Feb. 28, when a date for a bail hearing will be set.
Delisle, 40, faces two charges of violating the Security of Information Act that deal with communicating information that could harm Canada's interests.
Court documents say one of the alleged offences happened between July 6, 2007, and Jan. 13, 2012, while the other offence is alleged to have occurred between Jan. 10, 2012, and Jan. 13, 2012.
The Halifax man also faces a breach of trust charge under the Criminal Code, alleged to have taken place between July 6, 2007, and Jan. 13, 2012.
All the offences are alleged to have happened in or near Halifax, Ottawa and Kingston, Ont.
Up until 2010, Delisle worked for both the Chief of Defence Intelligence and at the Strategic Joint Staff, which oversees virtually every major aspect of the military's domestic and international plans and operations.
He joined the military as a reservist private in 1996 and was posted to the 3 Intelligence Company in Halifax.
He went on to join the regular forces in 2001, was promoted to sergeant before being accepted at university for two years in Kingston, Ont., as an officer candidate and eventually landed back in Halifax at the army's Atlantic headquarters.
In August of last year, Delisle was posted to Trinity, a highly-secure naval intelligence centre in Halifax.