John Murray, a Salvation Army spokesman, told a news conference in Toronto that the alleged theft was first discovered in August.
"A few months ago, the Salvation Army was tipped off about some irregularities at our warehouse and distribution centre right here on Railside Road," he said.
"As our investigation progressed, we discovered that we have been victims of an alleged theft and fraud that might eventually total several million dollars."
The organization has reported to police an alleged theft of $2 million worth of toys, as well as an undetermined amount of food and donated products.
Murray did not say what he thinks happened to the missing toys.
"In terms of what has happened to the toys, or where they go, certainly that's not the focus of our time here today and I would direct you to the Toronto Police Service," he said.
Toronto police Const. Tony Vella confirmed to CBC News that the alleged theft is under investigation.
"It's going to take us some time. It's a really complex case," Vella said Wednesday.
The Salvation Army has hired KPMG to conduct a forensic audit, which among other things will try to sort out where the toys might have gone.
Edward Nagel, a forensic accountant, told CBC News a network of individuals would likely have been needed to help turn so many toys into cash.
"You've got to have involvement on the outside, with sophisticated distribution channels set up to release that type of volume of gifts or donations," Nagel said.
Murray said the Salvation Army has taken steps to tighten security at its Railside Road facility and has terminated a staff member.
Alleged theft occurred over 24 months
The Salvation Army has "no reason to believe" theft has occurred elsewhere in the organization, Murray 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, that it was thought out," Murray said of the alleged toy theft.
"We believe it's happened over approximately a 24-month period of time."
While Murray said the Salvation Army expects to recoup most of the losses through insurance, the incident has stung the organization.
"I think from the Salvation Army's standpoint, quite honestly, it’s disheartening to be a victim of a crime," he said.
He called on the public to continue to support the Salvation Army, so that it can continue to help people in need.
Murray had recently been in Ottawa dealing with another case of theft within the Salvation Army.
He told CBC News earlier this week that $240,000 went missing from the charity's accounts in Ottawa.
The executive director of Ottawa's Salvation Army was fired after internal and police investigations.