TORONTO - Some Ontario hospitals fear they could be facing funding cuts after a worse-than-expected flu season drove up emergency room wait times this winter.

Tom Closson of the Ontario Hospital Association says some hospitals were so overwhelmed by flu patients, they couldn't meet ER wait time targets laid out by the province under its Pay for Results Program.

That could result in them having to pay money back to the Ministry of Health when their fiscal year ends March 31, said Closson, the association's CEO.

"I have heard from some hospitals their concern about whether they would potentially be clawed back under some of these performance schemes as a result of not being able to meet their targets due to the fact that it was an exceptionally challenging flu season," he said.

In July, the province pledged $100 million to help 71 high volume ERs cut the length of time patients wait for treatment. About $60 million of that was to go toward adding or reorganizing staff and renovating ERs to improve patient flow. The other $40 million was put in an "incentive" fund to reward hospitals that improve their wait times.

The Ministry of Health recovers a percentage of program funding from a hospital that fails to deliver based on how far off it was from hitting its targets, but a spokesman said seasonal fluctuations are considered.

The Southlake Regional Health Centre in Newmarket, north of Toronto, expects to lose some money.

Interim president and CEO Dr. Louis Balogh said the hospital saw a surge of flu-related patients in its emergency room in December and January.

"We did see an increase in our wait times and therefore expect a drop in pay-per-performance," said Balogh. "Despite that, we will be on the positive side. We expect to get less money than we would have otherwise received, but we will still be getting some."

Hospitals report their ER wait times to the government, which has set a target of four hours for minor conditions and eight hours for more complex conditions.

The health ministry said nine in 10 Ontario patients with complex conditions waited on average 11.5 hours in the ER in December and 12.5 hours in January. Those with more minor conditions waited 4.3 and 4.4 hours, respectively.

But for some, the wait in the ER for a bed in the hospital was much longer.

One in 10 patients admitted through the emergency department waited longer than 38.5 hours for a hospital bed in January, up from 35 hours in December. Part of the reason for that was the flu, said Closson.

Most experts weren't expecting the flu to hit as hard as it did in Ontario, which has recorded more than 5,200 laboratory-confirmed cases this season. That's almost triple the 1,791 cases seen in the last non-pandemic year in 2008-2009. The H1N1 pandemic dominated the health care scene a year ago.

"People were anticipating that after a pandemic we would have hardly any cases at all," said Dr. David Williams, Ontario's associate chief medical officer of health. "That hasn't been the case."

Only about 30 per cent of the public got a flu shot this year, down from 38 per cent in recent non-pandemic years, said Williams.

Flu-related hospitalizations topped 1,800 this season, compared to 213 two years ago.

"It was by far the worst year we've experienced in anybody's recent memory," said Dr. Michael Gardam of Toronto's University Health Network.

The flu meant the network's three downtown hospitals did not hit their wait time targets during the last quarter, said spokeswoman Gillian Howard.

Gardam said the three hospitals admitted almost 140 flu patients from mid-December to the end of January, compared with 65 flu patients all last year.

Surgical beds closed for the Christmas holidays were reopened for 30 flu patients, said Gardam.

At the London Health Sciences Centre, some patients waited 30 hours for a bed in January.

The flu led to more patients than usual being admitted in January and February, said hospital spokesman Neil Johnson. But he wouldn't say whether the hospital met its targets or if it expected to lose any money.

"We're certainly aware that if we don't meet targets, that the Ministry of Health can recover some of that money," said Johnson.

He said the hospital has spoken to the South West Local Health Integration Network, which administers funding from the ministry, about the flu's impact.

"They are aware of our concern though that this has been a unique year and that that may impact our ability to deliver on the improvements (in wait times) we wanted to do," said Johnson.