Minister of State Maxime Bernier told the House of Commons Monday the government will appeal the Quebec Superior Court decision.
On Sept. 10, Superior Court Judge Marc-Andre Blanchard voided two sections of the Conservative government's legislation to scrap the long-gun registry.
Blanchard ordered the federal government to give all records on Quebec-owned rifles and shotguns in the registry to the provincial government within 30 days.
The Conservatives have been adamant about scrapping the long-gun registry and destroying the existing data.
"The will of Parliament and Canadians has been clear," said Public Security Minister Vic Toews Monday, in a prepared statement. "We do not want any form of a wasteful and ineffective long-gun registry.
"The NDP has consistently said that if given the chance they would try and use this data to target law-abiding hunters, farmers and sport shooters in the regions of Quebec. Our Conservative government will always stand up for the rights of law-abiding gun owners."
The federal government has said in the past that any province that wants its own registry is welcome to start from scratch.