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Condominiums built along the waterfront in the west end of Toronto between the Humber River and Humber Bay Park East, are pictured on Jan. 26, 2017.Fred Lum/The Globe and Mail

Thousands of property taxpayers in Toronto were double-billed Wednesday after a computer problem caused two automatic bank withdrawals.

Affected taxpayers who suddenly found themselves short hundreds of dollars called to complain about the mix-up in the morning. By the afternoon, officials said, the city's bank, Royal Bank of Canada, was rolling back all of the errant payments.

In all, city officials said, 44,000 taxpayers enrolled in the city's two- and six-instalment pre-authorized payment program were caught up in the erroneous tax hike – just weeks after city council spent hours debating this year's rate increase and voting to hold it below the rate of inflation.

Casey Brendon, the city's director of revenue services, said the city normally sends a file with all the taxpayers and their bills to the bank via an automated system. Somehow two files ended up being sent to the bank. Exactly what happened is under investigation.

"There was an error in the processing of these files – in the city transmitting these to our banking service provider," Mr. Brendon said. "So it was inadvertently processed."

Asked whether the city or the bank was to blame, he replied: "We're still determining how this happened."

The city is reviewing its protocols for how it transmits the files, he said, noting that it has not happened before. Mr. Brendon also said that since the problem was fixed on the same day, nobody should have been charged fees for having insufficient funds in their account as a result of the error. Anyone who did should contact the city, he said, and Toronto would make them whole.

"The city apologizes for the inconvenience this may have caused to our customers," Mr. Brendon said.

Computer engineer Chris Hylarides, 36, a downtown condo owner, said he contacted the city after his wife noticed that two $1,200 payments had been sucked out of his bank account instead of one. As of 6 p.m. Wednesday, he still had not seen any sign of a refund, despite the city's statements to the media that the problem had been rectified.

But Mr. Hylarides said he wasn't concerned and assumed his refund would come through in a few days.

"I would like to know how it happened," he said. "But I suspect they won't tell us."

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