"It is in the best interest of the public that Monaghan not be compelled to act in conflict with his religious beliefs," Zatkoff wrote.
Monaghan is a Roman Catholic and said in his suit that he considers contraception a "gravely immoral" practice. He offers employees health insurance that excludes coverage for contraception and abortion.
The new federal law requires employers to offer insurance that includes contraception coverage or risk fines. According to Zatkoff's order, Domino's Farms faced $200,000 in yearly payments under the law. Employers have until Aug. 1 to comply with the law.
U.S. Department of Health and Human Services spokeswoman Erin Shields said Thursday night that she couldn't comment on the matter because the litigation is still pending.
In its response to the suit filed in December, the department denied the health care law had a substantial effect on Monaghan's exercise of his rights to religious freedom or freedom of speech.
The provisions of the health care law "are narrowly tailored to serve two compelling government interests: improving the health of women and children, and equalizing the provision of preventive care for women and men so that women who choose to can be a part of the workforce on an equal playing field with men," the government said.
Erin Mersino, a lawyer for the Thomas More Law Center, a conservative Christian legal defense group that represented Monaghan, noted that the law requires employers to offer health coverage that includes access to the morning-after pill and similar emergency contraception pills.
The morning-after pill works by preventing ovulation or fertilization. Critics of emergency contraception say it is the equivalent of an abortion pill because it can prevent a fertilized egg from attaching to the uterus. In medical terms, pregnancy begins when a fertilized egg attaches itself to the wall of the uterus.
"The HHS mandate forces our clients to provide abortion-causing drugs to their employees when doing so is a direct violation of the teachings of the Catholic Church and our clients' sincerely held religious beliefs," Mersino said.