Generally, employers are permitted to enforce mandatory flu vaccine policies, with some cautionary notes.
The Equal Employment Opportunity Commission ("EEOC") has said that employers should “consider simply encouraging employees” to get the flu vaccine rather than requiring it. (See “Pandemic Preparedness in the Workplace and the Americans with Disabilities Act” guidance at http://www.eeoc.gov/facts/pandemic_flu.html, question 13.) The EEOC’s concern is that any mandatory policy would have to yield to a request for a reasonable accommodation from either (1) an employee whose disability prevents him from getting a flu vaccine (e.g., someone with a severe egg allergy, as most flu vaccines are cultured using eggs), or (2) an employee whose sincerely held religious beliefs, practices, or observances prevent him from taking the vaccine.
Notwithstanding the EEOC’s concerns, so long as the employer allows for reasonable accommodations--which could include having employees wear masks during flu season instead of getting a flu shot-- there should be no problem under federal law with a mandatory policy. However, employers should take care to ensure that there is not a state privacy law that might be implicated by a mandatory flu shot program. And, if the employer’s work force is unionized, the result could be different; some courts have found that a mandatory vaccine policy is something that must be bargained for with the union and cannot be unilaterally imposed.