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The Public Employees Federation is asking a court to reverse a policy requiring vaccination for the seasonal and swine flu viruses.
The health department said the workers must be vaccinated by November 30 or face possible disciplinary action, including dismissal.
"In two weeks the Department intends to vigorously defend this lawsuit on its merits and we are confident that the regulation will be upheld," the health department said in a statement after today's order.
PEF says it encourages its members to be vaccinated against the flu, but opposes the emergency regulation requiring the vaccine as a condition of employment.
The union says about 5,000 of its members are covered by the emergency regulations.
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