A federal judge has issued a ruling siding with the Obama administration saying that it has the right to force Hobby Lobby, a Christian-owned and run company, to pay for drugs for women that may cause abortions.

The privately held retail chain with more than 500 arts and crafts stores in 41 states filed a lawsuit against the Obama administration over its HHS mandate. The company says it would face $1.3 million in fines on a daily basis starting in January if it fails to comply with the mandate, which requires religious employers to pay for or refer women for abortion-cause drugs that violate their conscience or religious beliefs.

The lawsuit was filed in the US District Court for the Western District of Oklahoma and the business says it is opposing the Health and Human Services “preventive services” mandate, which it says forces the Christian-owned-and-operated business to provide, without co-pay, the “morning after pill” and “week after pill” in their health insurance plan, or face crippling fines up to 1.3 million dollars per day.

“By being required to make a choice between sacrificing our faith or paying millions of dollars in fines, we essentially must choose which poison pill to swallow,” said David Green, Hobby Lobby CEO and founder. “We simply cannot abandon our religious beliefs to comply with this mandate.”

However, U.S. District Judge Joe Heaton issued a ruling late Monday rejecting Hobby Lobby’s request to block the mandate. Judge Heaton said that the company doesn’t qualify for an exemption because it is not a church or religious group.

“Plaintiffs have not cited, and the court has not found, any case concluding that secular, for-profit corporations such as Hobby Lobby and Mardel have a constitutional right to the free exercise of religion,” the ruling said.

Heaton wrote that “the court is not unsympathetic” to the company’s desire to not pay for abortion-causing drugs but he said the Obamacare law

“results in concerns and issues not previously confronted by companies or their owners.”

“The question of whether the Greens can establish a free exercise constitutional violation by reason of restrictions or requirements imposed on general business corporations they own or control involves largely uncharted waters,” Heaton wrote.

Hobby Lobby plans to appeal the ruling, according to a pro-life legal group that notified LifeNews of the ruling.

“Every American, including family business owners like the Greens, should be free to live and do business according to their religious beliefs,” Kyle Duncan, general counsel for the Becket Fund for Religious Liberty, said. “We disagree with this decision and we will immediately appeal it.”

The court did not question that the Green family has sincere religious beliefs forbidding them from participating in abortion. The court ruled, however, that those beliefs were only “indirectly” burdened by the mandate’s requirement that they provide free coverage for specific, abortion-inducing drugs in Hobby Lobby’s self-funded insurance plan.

Duncan previously talked about what the Obama administration told the court:

The administration’s arguments in this case are shocking. Here’s what they are saying: once someone starts a “secular” business, he categorically loses any right to run that business in accordance with his conscience. The business owner simply leaves her First Amendment rights at home when she goes to work at the business she built. Kosher butchers around the country must be shocked to find that they now run “secular” businesses. On this view of the world, even a seller of Bibles is “secular.” Hobby Lobby’s affiliate, Mardel, sells Bibles and other Christian-themed material, but because it makes a profit the government has now declared it “secular.”

The administration’s position here — while astonishing — is actually consistent with its overall view of the place of religion in civil society. After all, this is the administration who argued in the Hosanna-Tabor case last year in the Supreme Court that the religion clauses of the First Amendment offered no special protection to a church’s right to choose its ministers — a position that the Court rejected 9-0. This is the administration which has taken to referring to “freedom of worship” instead of “freedom of religion” — suggesting that religious freedom consists in being free to engage in private rituals and prayers, but not in carrying your religious convictions into public life. And this is the administration who crafted a “religious employer” exemption to the HHS mandate so narrow that a Catholic charity does not qualify for conscience protection if it serves non-Catholic poor people.

As you point out, the administration is trying to justify its rigid stance against religious business owners by saying otherwise they would become a “law unto themselves,” and be able to do all sorts of nasty things to their employees — like force them to attend Bible studies, or fire them if they denied the divinity of Christ. Nonsense. Hobby Lobby isn’t arguing for the right to impose the Greens’ religion on employees, nor for the right to fire employees of different religions. There’s already a federal law that protects employees from religious discrimination and that’s a very good thing. This case is about something entirely different: it’s about stopping the government from coercing religious business owners. The government wants to fine the Greens if they do not violate their own faith by handing out free abortion drugs, and now it’s saying they don’t even have the right to complain in court about it

Duncan said the onerous provisions of the HHS mandate “will hit Hobby Lobby in about two months — on January 1, 2013. At that point, it will face the choice of dropping employee health insurance altogether (and paying about $26 million a year in penalties), or continuing its current plan (which will expose it to about $1.3 million in fines per day). So it is not hard to imagine why the Greens felt they had no choice but to go to court.”

There are now 40 separate lawsuits challenging the HHS mandate, which is a regulation under the Affordable Care Act (aka “Obamacare”). The Becket Fund led the charge against the unconstitutional HHS mandate, and along with Hobby Lobby represents: Wheaton College, East Texas Baptist University, Houston Baptist University, Belmont Abbey College, Colorado Christian University, the Eternal Word Television Network, and Ave Maria University.

Hobby Lobby is the largest and the biggest non-Catholic-owned business to file a lawsuit against the HHS mandate, focusing sharp criticism on the administration’s regulation that forces all companies, regardless of religious conviction, to cover abortion-inducing drugs. It has faced a small boycott from liberals upset that it would challenge the mandate in court.

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The Obama admin says there is an exemption in the statute but Duncan says that is not acceptable.

“The safe harbor’s protection is illusory,” said Duncan. “Even though the government won’t make religious colleges pay crippling fines this year, private lawsuits can still be brought, schools are at a competitive disadvantage for hiring and retaining faculty, and employees face the specter of battling chronic conditions without access to affordable care. This mandate puts these religious schools in an impossible position.”

Last week, a federal court stopped enforcement of the Obama administration’s abortion pill mandate against a Bible publisher which filed a lawsuit against it — the third such victory.