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Conservative leader Doug Ford makes a campaign stop in Ottawa on May 30.Sean Kilpatrick/The Canadian Press

The Ontario government handed out COVID-19 vaccine clinic contracts to companies, including one run by large Progressive Conservative Party donors, that wasted shots or delivered just a fraction of their expected doses, the province’s Auditor-General says.

In her annual report released on Wednesday, Auditor-General Bonnie Lysyk also singles out the government of Premier Doug Ford for inaction on flooding and environmental protections, and says the office of his minister of transportation overrode the ministry’s own technical experts to fast-track two highway projects.

Much of the auditor’s focus was on the province’s response to the COVID-19 pandemic. She concludes the province’s decentralized vaccine booking system was “unco-ordinated,” resulted in “confusion” and prompted many to “vaccine shop,” contributing to 227,000 no-show appointments last year.

The Auditor-General does say most contracts related to COVID-19 appear to have been handled appropriately, “given the urgency of the pandemic.” But she said in some cases, sole-sourced deals awarded without competition resulted in a waste of money, vaccines or both.

Her audit says the Ministry of the Solicitor General – headed by Sylvia Jones at the time, who is now Minister of Health – sole-sourced a contract in January to a company called FH Health to operate COVID-19 vaccination clinics at nine Toronto-area locations, including one at the Toronto Zoo, aimed at education workers.

The company had approached the ministry directly, the auditor says, and got the nod as it already had similar government contracts. But its clinics were barely used, according to the Auditor-General, with only 6 per cent of daily available appointments taken up from January to March, 2022.

The Opposition NDP had earlier this year demanded an investigation after it was revealed that FH Health officials gave the governing Progressive Conservatives thousands of dollars in political donations. Ms. Lysyk’s report says at least 18 individuals, including company board members and employees, and those sharing names with them and their family members, gave $54,000 to the PCs in September, 2021, before the contract was awarded.

Ms. Lysyk recommends that government ministries be required to “document what safeguards they must use to prevent bias and perceived and actual conflicts of interest” in awarding sole-sourced contracts.

Another company, Switch Health, was paid $17.3-million to run two vaccination clinics, including one near Pearson International Airport aimed at arriving foreign agricultural workers, but wasted 57 per cent of its vaccines, or 58,859 doses, the audit found.

Speaking to reporters, Ms. Jones defended her government’s vaccination record.

“We very strategically made sure that, as we saw communities that needed additional assistance, we put the financial resources in to get that job done,” Ms. Jones said, arguing that while some vaccines were wasted, the contracts ensured vaccination clinics could be set up quickly and target those who needed them most.

A strategy to target certain COVID-19 hot spots, often lower-income or racialized communities where transmission was higher, missed key areas, the audit found. And doctors were paid much more to vaccinate patients than other health professionals, the audit says. The Ministry of Health paid doctors $170 to $220 an hour to jab patients at vaccinations centres, much less than the $32 to $49 an hour it paid nurses.

On testing, Ms. Lysyk also found problems. She concludes the government did too little to ensure hundreds of thousands of rapid test kits distributed to businesses and other groups were actually used before the government sent out more of the at-the-time scarce tests.

And she says better co-ordination of testing clinics set up by the Ministry of Education and the Ministry of Health could have saved more than $18-million. In all, the two ministries paid private firms $32-million to operate the clinics from January to June, 2021. But the Ministry of Education’s facilities only tested between 2 and 7 per cent of their capacity, on average. They were also guaranteed minimum payments of up to $8,255 a day. And more than 100 times, the report says, they were paid for doing no tests.

Ms. Lysyk also found that $66-million of personal protective equipment, such as masks, expired or was damaged in 2021-22 – even after expirations of stockpiles at the pandemic’s outset caused governments to scramble.

In her audit of highway planning, the auditor says the office of Mr. Ford’s Minister of Transportation – Caroline Mulroney since June, 2019 – overruled ministry experts and pushed lower-priority projects ahead, including the Toronto-area Highway 413 and Bradford Bypass that were centrepieces of the government’s spring re-election campaign.

The report says the Bradford Bypass, which would connect Highways 404 and 400 north of Toronto, had only been deemed “medium” priority. The audit also estimates its cost at between $2-billion and $4-billion, much higher than previous public estimates. Highway 413, which would encircle Toronto to the west, had been labelled “high priority,” but ministry experts had decided not to request funding because it still faces a lengthy federal review. The auditor says the 413 has an estimated cost of $4-billion.

Speaking to reporters, Ms. Lysyk said the changes were not because of any undue “political interference” but that the government should be more transparent when politicians override advice from civil service experts.

Her report also includes a range of critical findings about the PC government’s environmental record, concluding that Ontario is doing far too little to combat invasive species, which cause $3.6-billion in damage a year, protect Ontarians from flooding or protect the ecologically sensitive Niagara Escarpment.

She also concludes that the province is doing too little on the risks posed by inactive oil and gas wells, even after the explosion caused by a leaking well last year in Wheatley, Ont., destroyed two buildings and injured 20 people.

Ms. Lysyk says too few wells are being inspected, and that the Ministry of Natural Resources and Forestry does not know whether it is focusing on the riskiest of the 27,000 such oil and gas wells across the province. Her report estimates that 36 per cent of those wells, many plugged with substandard materials before 1970, could be dangerous. Three high-risk wells have been leaking since 2018, the report says, but only one was scheduled to be sealed in 2022-23.

Natural Resources Minister Graydon Smith has said his ministry is working on a new strategy to deal with the problem. He reiterated Wednesday that the strategy could not proceed until a consultants’ report on the Wheatley disaster is complete.

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