The case was launched in 2013 after Health Canada sent letters to people with the program's name on the envelope. Before that, mail sent to people in the program didn't mention marijuana.
Recipients were upset, saying their privacy had been violated. Some said they worried they'd lose their jobs or be victims of a home invasion.
In March of this year, the Office of the Privacy Commissioner of Canada ruled that Health Canada had violated federal privacy laws. That ruling didn't allow for any compensation.
In a press release, the Halifax law firm that launched the case says the certification shows the Federal Court has decided the class action lawsuit is necessary to allow people access to justice.
The plaintiffs are seeking damages for breach of contract, breach of confidence, invasion of privacy and Charter violations.
"This is not over yet, but the thousands of affected program members should take some comfort that every legal claim we advanced on their behalf has been approved to go forward," said David Fraser of McInnes Cooper.
McInnes Cooper is jointly representing users from across Canada with Branch MacMaster LLP of Vancouver, Charney Lawyers of Toronto and Sutts, Strosberg LLP or Toronto and Windsor.
David Robins of Sutts, Strosberg LLP says more than 1,000 people have registered on an online site for the lawsuit to explain how the breach affected them.
The federal government now has 30 days to appeal the Federal Court's certification.