"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.