The Salvation Army has allegedly been the victim of an intricate fraud, robbing it of more than $2 million in toys from its Toronto warehouse over the course of two years, charity officials say.

The agency fired the executive director of the warehouse Monday. He was put on paid leave shortly after a whistleblower employee came forward in mid-August. His firing came as the result of an internal audit, said Maj. John Murray of the Salvation Army.

Food and other donations are alleged to have disappeared as well.

“At the root of it, it’s about deception and about deceiving people and organizations and it would appear from everything I’ve seen and know about it, it was very sophisticated, it was intentional, well planned out,” Murray said.

The 2011 Sunshine List, which lists public sector employees making more than $100,000 per year, names David Rennie as executive director of the warehouse facility on Railside Rd. He made $111,215 that year.

While Murray refused to confirm the name of the executive director, he said the person who was fired had been in the position since February 2010.

Attempts to reach Rennie Tuesday night were unsuccessful.

Murray declined to comment on whether or not any other employees may have been involved, saying there is an ongoing Toronto police investigation. No charges have been announced.

Police are expected to release details Wednesday.

Murray said the anonymous whistleblower, believed to be an employee at the warehouse, reported “irregularities” at the Railside Rd. facility, near Lawrence and Victoria Park Aves.

The warehouse was responsible for receiving, sorting and distributing both food and toy donations to needy families.

“It took the strength of a whistleblower to bring it forward,” said Murray, who noted the facility processes about seven million tonnes of food and products each year. “I think it really speaks to their character and we’re very pleased, and frankly indebted to them, that they did this.”

Murray said the theft was something that would have evaded their usual security procedures.

“The Salvation Army took immediate actions at the Railside facility,” said Murray, noting they changed the locks, reset the cameras and reprogrammed security within 24 hours of the audit being conducted.

It is not known what became of the missing toys.

Bettylynn Stoops, a retired civil servant with more than 30 years of experience, will start as executive director of the Railside facility next week.

Meanwhile, another audit on one of the Salvation Army’s centres in Ottawa resulted in the firing of its executive director when $250,000 was found missing from the operating budget.

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It’s believed the money was taken over several years. Executive director Perry Rowe had been with the centre for eight years prior to the incident.

Murray said the two incidents are unrelated, but that “the timing obviously is difficult and will certainly perhaps raise questions for people.”

Barb Mrozek, director of Toronto Star Charities and Philanthropy, was shocked to hear about the Salvation Army’s loss.

“I can’t imagine what they are going to do,” she said Tuesday night. “I would probably have a heart attack.”

To put the $2 million loss in context, the Toronto Star Santa Claus Fund is raising $1.6 million this Christmas to provide gift boxes to 45,000 children — including about 35,000 on welfare and another 10,000 referred to the fund through community agencies and the city’s shelter system.

The $2-million lost would provide Star Christmas boxes for every needy child whose family wanted one.

The Salvation Army plans to address the public at a news conference Wednesday afternoon at the Railside warehouse.

The warehouse suffered a massive loss in 2008 when a blaze destroyed toys and food. There were no injuries or damage to the structure, but the depot lost much of what was to be given out around Christmastime that year.

Murray noted the theft at the warehouse isn’t going to affect this year’s distribution of toys and food because it was spread out over the past two years.

“We do have toy product in the warehouse ready to go for our Christmas program,” he said. “We’re good to move forward but the reality is that the Salvation Army is going to work very hard to ensure and reassure people in terms of the public trust.”

With files from Laurie Monsebraaten, Daniel Dale, Jayme Poisson, Marco Chown Oved and The Canadian Press