Vic Toews called the ruling an "absolute victory for the rule of law."
The Toronto court had heard a motion from the Barbra Schlifer Commemorative Clinic for an emergency injunction that would have prevented the federal government from destroying long-gun data in a federal registry that's been abolished.
Justice D.M. Brown declined to grant the injunction, rejecting arguments that the destruction would be a violation of the Charter of Rights.
The City of Toronto had supported the motion, though the province did not.
The ruling follows a successful court application by the Quebec government to preserve long-gun registry data in that province.
Last week, Superior Court Judge Marc-Andre Blanchard voided two sections of the Conservative government's legislation to scrap the long-gun registry.
The judge ordered Ottawa to surrender all records on Quebec-owned rifles and shotguns in the registry to the province within 30 days.
Minister of State Maxime Bernier told the House of Commons on Monday the government will appeal the Quebec court decision.
The Conservative government has said that any province wanting its own long-gun registry is welcome to create one from scratch.
"We were very pleased that the Ontario Superior Court has ruled in favour of law-abiding hunters, farmers and sport shooters," Toews said in a statement Friday.
"The will of Parliament and Canadians has been clear. We do not want any form of a wasteful and ineffective long-gun registry."
An outspoken proponent of the registry said the fight will continue.
"This decision is a setback but we will continue to fight for sensible controls on rifles and shotguns," Wendy Cukier of the Coalition for Gun Control said in a statement.
"Information about who owns what guns is essential to reducing the diversion of guns to illegal markets and the registry data has been shown to be useful in solving crimes."Suggest a correction