The court stayed a motion brought by Canada's National Firearms Association and a Quebec gun dealer, saying federal legislation abolishing the registry is still under litigation.
The Conservative government in Ottawa abolished the registry last year but Quebec fought to preserve the provincial data, saying it wanted to start its own gun registry.
The Quebec Court of Appeal ruled the federal legislation was valid and that the data should be destroyed — as it has been elsewhere in Canada — but the province is seeking a leave to appeal the case to the Supreme Court of Canada.
The long gun registry remains in effect in Quebec as the provincial government argues the law is unconstitutional.
Federal Court judge Sean Harrington says it would be "entirely inappropriate" to order the destruction of records that are the heart of an ongoing court appeal.
Harrington noted in his written decision that the applicants had anticipated his ruling and wanted him to deny police access to the existing records, and also keep any further data from being compiled on long gun transfers within Quebec.
"The Attorney General of Canada objected to the amendment on the basis that he would have to seek instructions as to the implications thereof," Harrington wrote.
"On the basis that if Quebec ultimately succeeded, I pointed out that there would be a gaping hole in the records."