He garnered the majority of Catholic votes in the 2008 election, but a number of Catholic groups now say President Obama is showing a complete lack of regard for their beliefs.
They count his decisions to lift restrictions on abortion and stem cell research among the most offensive.
"As far as the Catholic church goes, there's no bigger priority for Catholics than human dignity and human life," said Cathy Ruse, senior fellow at the Family Research Council said. "And the Obama administration has just been an assault on those values again and again in just two months."
But some American Catholics support the president, saying his policies are consistent with their "mainstream" beliefs.
"President Obama has already reached out and won the Catholic vote," Jon O'Brien, president of Catholics for Choice, said.
"That's what happened in the last election in spite of the very loud voices of some extreme uber-Catholics who really want to paint this black and white picture -- to engage us in this endless culture war," he said.
O'Brien, whose group supports access to contraception and abortion, said Obama presented Catholic voters with a social justice agenda they can support.
One of the four main priorities of Obama's faith-based office is to find ways to reduce the abortion rate, an attempt at common ground. But shortly after taking office, Obama lifted restrictions on federal funding of international family planning groups that perform abortions or provide information about the procedure.
Then in late February, the administration said it would rescind broad protections put in place in the waning days of the Bush administration for health workers who refuse to provide care they find objectionable on personal, moral or religious grounds.
The White House has said the administration was committed to protecting the rights of health care workers who don't want to perform abortions, but was concerned the Bush language went too far and could restrict services such as family planning and infertility treatments.
Obama's reversal this month of Bush-era restrictions on federal funding for embryonic stem cell research is the latest disappointment for conservative Catholics.
Obama's nomination of Kansas Gov. Kathleen Sebelius, Catholic who supports abortion rights in conflict with church teachings, for health and human services secretary also has stirred the old culture war divisions.
Catholic leaders warn that congregants cannot effectively walk a tight rope between the beliefs of the church and also support presidential policies that contradict them.
"It would be like claiming to be a vegetarian and ordering a ham sandwich," the Rev. Gerald Murray of the Church of St. Vincent de Paul in New York City said. "They're incompatible, you can't do it."
Murray also worries about Obama's decision to roll back a federal regulation that would give added protection to health workers who object to performing procedures like abortion on the basis of moral objections.
Murray said the Church will vigorously oppose the move, and calls it a "gross violation of religious liberty" not only for Catholics, but also for everyone who believes abortion is a sin.
Catholic hospitals are spread nationwide and provide health care to millions, but Murray warns they will shut down before being forced to allow abortions.
The Associated Press contributed to this report.