The Department of Justice filed a lawsuit Tuesday alleging that a county-owned nursing home in Wisconsin discriminated against a former employee's religious objections to receiving a flu vaccine.

The suit alleges that Barnell Williams, a former nursing assistant at Lasata Care Center, requested an exemption from a center policy requiring flu vaccinations "because of her sincerely held religious belief that Bible-based scriptures prohibited flu shots," according to a statement from the department.

The center did allow employees to opt out on the basis of religion, but only if they could provide a written statement from their clergy leader assenting to the request. Williams could not acquire such a letter, as she did not belong to a church with a clergy member, and was denied an exemption, the statement says.

An administrator at the center did not immediately respond to CNBC's request for comment on the suit. A receptionist, however, told CNBC that Ralph Luedtke, who allegedly told Williams to "consider this your last day" if she did not receive the shot, is no longer the campus administrator.

Williams, according to the suit, submitted to the flu shot after allegedly being told that refusing to do so would result in her termination. However, Williams' failure to either meet the exemption requirement or accept the flu shot was deemed a "voluntary resignation" under the policy, according to the complaint.

The complaint also alleges that Williams experienced "severe emotional distress" and suffered sleep problems, anxiety and "fear of 'going to Hell.'"

"When employees' religious principles conflict with work rules, they should not have to choose between practicing their religion and keeping their jobs if a reasonable accommodation can be made without undue hardship to the employer," acting Assistant Attorney General John Gore for the Civil Rights Division said in the statement.

The Justice Department's suit argues that the requirement to obtain a letter from a clergy member violates the Civil Rights Act of 1964, the federal law protecting employees against discrimination by employers on the basis of race, gender and religion, among other protections. The DOJ alleges that the requirement caused an "undue hardship" for Williams.

In October 2016, Williams filed a charge with the Equal Employment Opportunity Commission alleging religious discrimination, which was then referred to the DOJ.

The plaintiff is seeking compensatory damages for Williams, "in addition to injunctive and other appropriate relief."