Police have been investigating the alleged theft, estimated to be worth about $2 million, since late September, but have not made any arrests.
The news comes as the Salvation Army is preparing to start its annual Christmas Kettle Campaign, where volunteers solicit donations in high-traffic areas like shopping malls and on the street.
About 140,000 toys are distributed to families in need each holiday season from the Toronto warehouse, but spokesman John Murray said at a news conference Wednesday that no one will go without.
"I can assure you that anyone in need this Christmas will be helped by the Salvation Army," he said.
"To those Canadians who routinely and generously give to the Salvation Army I would appeal to you this afternoon to not lose confidence in the work of the Salvation Army and the work that we do on your behalf in Canadian cities."
A whistleblower within the organization tipped the Salvation Army off a few months ago and internal auditors made the "troubling" discovery, Murray said.
Executive director David Rennie was then fired. No criminal charges have been laid.
Meanwhile, the executive director at the Salvation Army in Ottawa has been fired after auditors discovered $250,000 has gone missing. Perry Rowe had been with the charity's Booth Centre for eight years.
Police have not yet determined what happened to the toys at the Toronto warehouse. Murray said the Salvation Army believes no other locations have been hit with alleged thefts.
"This is an isolated situation," he said. "We believe that it's been very specific. It's been targeted. It's been very strategic in the way that it was put together. It was thought out."
The warehouse has video surveillance and security systems, but the Salvation Army has retained KPMG to do an audit to determine what other checks and balances can be put in place.
The security system is good, so the alleged theft signals that when there is a will, there is a way, Murray said.
"If an individual wants to defraud an organization there are ways and means to do that," he said.
The hearts of people at the Salvation Army go out to whoever committed the alleged theft, but if people have problems in their lives they should instead come to the organization for help, Murray said.
"I also would remind people that when you're stealing from an organization like the Salvation Army, you're not stealing from the Salvation Army," he said. "You're stealing from those people who the Salvation Army helps every day and in Canada that's 1.8 million Canadians in 400 Canadian communities."