The TTC's largest union has lost its bid to block a COVID-19 vaccination policy that could see thousands of employees placed on unpaid leave.

Earlier this month, the Amalgamated Transit Union (ATU) Local 113 asked the Ontario Superior Court to grant an injunction that would prevent the mandatory vaccine policy from being implemented for a period of up to 60 days.

At the time, the union argued that the pause would give an auditor time to make a decision on a grievance filed over the policy.

In a news release issued Saturday, ATU confirmed the court denied their request.

"We are very disappointed with the court's decision to deny our request to suspend operation of the TTC's mandatory vaccination policy," President of ATU Local 113 Carlos Santos said in a statement.

"We believe the TTC's policy of suspending and terminating unvaccinated workers is unfair and will be struck down at arbitration. While I had hoped the court would put a stop to this policy while we fought in arbitration, I am confident we will ultimately prevail."

TTC staff were given until Nov. 20 to get both doses of a COVID-19 vaccine. As of today, 90 per cent of the transit agency's 15,061 employees have disclosed their status.

According to the TTC, employees who are either unvaccinated or have not shared their status by the end of Nov. 20 will be placed on unpaid leave until they receive their shots. Employees could be terminated if they do not comply by Dec. 31.

It is unclear how many employees will be placed on unpaid leave as of Sunday, but Santos told CTV News Toronto that he knows of just under 2,000 workers who will be impacted.

"It's around 1,200 operators, 500 or 600 maintenance personnel, which varies from a different variety of jobs," he said, adding that he doesn't ask members why they don't want to get the COVID-19 vaccine.

"We do encourage vaccination, we do know that it minimizes risk, but at the end of the day, our members have to make the decision on their own."

As a result of a potential staff shortage, the TTC has reduced service on several routes starting Nov. 21.

"I want to thank all the employees who have complied with the Policy and I want to thank all our customers for their support. Together we will get through this," TTC's CEO Rick Leary said in a statement issued Saturday.

"We know that getting vaccinated is one of the most important things that people can do to put the pandemic behind us. As an essential service, we need the TTC to be a safe place for everyone.

Santos said the injunction was never about vaccinations but rather about saving jobs "while still protecting public health." To do this, he suggests implementing a COVID-19 testing regimen for unvaccinated employees similar to what is being done with Mississauga Transit and Brampton Transit.

"We believe that instead of firing workers and cutting service, the TTC should be offering regular testing for the small percentage of workers who do not wish to receive the vaccine," he said.

"Not only are our members not able to provide food on the table for their families, but they are now not serving the citizens of Toronto with public transit and they're actually creating an even bigger crisis and a bigger health and safety risks by now having less service out there and more overcrowding."

Santos said that ATU will continue to fight the policy through an arbitration process.