"We cannot – we will not – comply with this unjust law," O'Brien wrote in the letter, which was read during last Sunday's Mass at the area's 153 Roman Catholic parishes.
The agency recently rejected a request by Catholic groups to be exempt from a requirement that insurance cover contraception and sterilization — areas that go against the church's teachings. The Obama administration has given the religious groups a year to comply with the law.
But O'Brien said in his letter that the yearlong reprieve was a weak concession.
"The Administration has cast aside the First Amendment to the Constitution of the United States, denying to Catholics our nation's first and most fundamental freedom, that of religious liberty," O'Brien wrote.
The letter was O'Brien's strongest condemnation of the rule, which most employers have to comply with this year. It comes as Catholic groups are putting increased pressure on federal officials to reverse their opinion. The Baltimore Archdiocese was one of many around the country that issued letters to its members criticizing the rule and urging them to speak out against it.
Alina Salganicoff, vice president and director of women's health policy at the Kaiser Family Foundation, called O'Brien's position "a very strong stance."
The controversy over birth control coverage has erupted as Obama prepares for re-election, and some say his position could alienate segments of the 70-million registered Catholic voter population.
Obama's re-election team, meanwhile, is showing indications of compromise. David Axelrod, a key adviser in Obama's campaign, said the administration would be willing to work with Catholic universities and hospitals to implement the new rules.
He said the yearlong grace period should allow religious institutions to offer contraception coverage without going against their religious beliefs.
"We certainly don't want to abridge anyone's religious freedom, so we're going to look for a way to move forward that both guarantees women that basic preventive care that they need and respects the prerogatives of religious institutions," Axelrod said Tuesday on MSNBC's "Morning Joe."
Catholic leaders seemed open to the right kind of compromise.
"While we welcome any acceptable solution, it cannot infringe on the protection of conscience and religious freedom," said Sean Caine, a spokesman for the Archdiocese of Baltimore.
The Obama administration mandated coverage of birth control last year as part of a list of preventive services that insurers should cover without additional co-pays or deductibles. Also included on the list are exams for breast and colon cancers and sexually transmitted diseases. The new rules become effective beginning in August as insurance plans begin to renew.
The contraception rules are supported by women's groups. The U.S. Department of Health and Human Services said they are necessary to improve access for health services to women.
Sen. Barbara A. Mikulski, who helped lead the effort to get preventive services for women included in health care reform, took to the Senate floor Tuesday to say that the birth control issue had been blown out of proportion.
The Maryland Democrat said getting lost in the debate is the fact that both women and men will benefit because it covers services like prostate exams. She said birth control was included at the advice of the National Institutes of Medicine, not for any political reason.
She also pointed out that religious institutions would not have to provide birth control, just to make it available under insurance. A Catholic women's college, for instance, wouldn't have to give out birth control in the student clinic.
"We have gotten off to the wrong debate — and the wrong discussion," Mikulski said. "Let's get back to how we improve the health care of women."
At least one poll shows that some Catholics may not agree with the leadership of the church on the issue. About 53 percent of Catholic voters support the requirement of birth control coverage by religious groups, according to a poll conducted by Public Policy Polling for Planned Parenthood. Planned Parenthood and the Catholic Church often clash over issues of birth control and abortion.
David Cloutier, associate professor of Mount Saint Mary's University in Emmitsburg, said the church is turning it into a broader issue of church freedoms, rather than just about birth control.
"There was very little in the letter about contraception," he said. "But there was great deal about the way in which religious freedom was being threatened."
Cloutier heard O'Brien's message read during Mass at St. John the Evangelist in Frederick. He said the church seems to feel that cutting off insurance would be the only way to "to follow the conscience of the institution."
The Archdiocese of Baltimore covers about 3,500 people who work for various Catholic schools and nonprofits. The institution has its own health insurance plan.
If it were to decide not to cover employees, those people would have to buy insurance from exchanges, or open markets that are being set up for people who aren't covered by employer insurance.
Salganicoff at the Kaiser Family Foundation said it would be more complicated for people to have to buy for the open market. She said it would also go against the purpose of health care reform to make coverage more accessible.
"The goal is to improve employee-sponsored coverage, not to put push people out of their workplace coverage," she said.
Employers will be required to pay varying fees if they don't offer insurance under health care reform. O'Brien said in his letter that that is something the archdiocese would be willing to do.
If the federal government doesn't agree to the changes, religious groups could file lawsuits in court or try to persuade Congress to change the provision legislatively.
For now, Caine said, the archdiocese will continue to ask its parishioners to call their elected officials to speak out against the birth control rule. The archdiocese is also staying in constant contact with U.S. Conference of Catholic Bishops to fight the issue.
Reuters contributed to this article.