In newly filed court documents, the government also contends that divulging the figure might damage relations with key allies, especially the United States.
Information Commissioner Suzanne Legault is challenging the government's refusal to disclose the data to a Montreal journalist who requested it under the Access to Information Act.
La Presse reporter Daphne Cameron filed two requests for figures from 2006 through 2010 — one for the total number of people on the list, the second for the number of Canadian citizens.
Legault's office investigated Cameron's complaint against Transport Canada and recommended last year that the agency release the figures.
Transport Canada refused to comply, prompting Legault to take the case to the Federal Court of Canada.
Under the no-fly program in place since June 2007, airlines rely on a list of individuals considered "an immediate threat to civil aviation" should they board an aircraft.
Candidates for the no-fly roster — formally known as the Specified Persons List — are put forward by the RCMP and the Canadian Security Intelligence Service.
Members of these agencies, along with representatives of Transport, the Canada Border Services Agency and the Justice Department, sit on an advisory panel that formally recommends names for inclusion. The public safety minister has the final say.
In withholding the numbers, Transport Canada invoked a section of the access law shielding information whose release could interfere with the conduct of international affairs as well as the detection, prevention or suppression of "hostile activities."
In her May 2013 letter to then-transport minister Denis Lebel, filed with the court, Legault said she was not satisfied the exemption had been properly applied.
Disclosing an aggregate number of people on the no-fly list "would not allow an individual to determine whether he or she is on the list," she wrote.
The roster is only one of a number of lists used by airlines to ensure aviation security, Legault added. Therefore, even if someone could conclude they were on the list, "this fact would not transform Canadian or Canadian-bound aircraft into 'soft targets,' as claimed by (Transport Canada)."
Christopher Free, a senior Transport Canada intelligence official, was consulted by Transport's Access to Information division in March 2010 on whether the figures could be disclosed. Free concluded the number of names "was valuable information for terrorist operational planning" and that its release would harm national security, he says in an affidavit filed recently with the court.
"This determination is based on my understanding of how terrorist groups operate," says Free, chief of operational and intelligence support within the aviation security operations branch of Transport.
"In order to plan and execute a successful attack and minimize risk, terrorist organizations must first solve the 'intelligence problem' of knowing and understanding the strengths, weaknesses and opportunities available with respect to their target."
Portions of Free's filing have been blacked out, with the court's permission, in keeping with federal concerns about maintaining secrecy.
The United States has revealed there are about 16,000 people — including fewer than 500 Americans — on its no-fly list.
Still, Free says disclosure of the Canadian numbers could "adversely affect our relations with key allies, and especially the U.S."
CSIS and Public Safety Canada back Transport's bid to keep the figures under wraps.
"Although the information may at first appear innocuous, the Service maintains that it would be ill advised to expose the scope of Canada's intelligence knowledge in this specific area of enforcement," CSIS says in an October 2011 memo that has become part of the court file.
In a 2012 report, the watchdog that keeps an eye on CSIS said confusion over how the no-fly list should work had "significantly undermined" its potential to help keep the skies safe.
The Security Intelligence Review Committee said the notion of "an immediate threat to civil aviation" was open to interpretation, and federal agencies had "struggled" with nominating people for the list.
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