The act requires non-profit groups that have health insurance plans to offer contraceptives.
Catholic bishops and priests across the country read out letters at Sunday mass denouncing the decision, calling it an attack on their religious freedom.
"Religion has always overcome obstacles, and I'm sure this will be one obstacle they can overcome as well," said Catholic church-goer John Robins.
The new rule is part of the health care overhaul passed in 2010. Starting August first, non-profit employers who, based on religious beliefs, currently do not provide contraceptive coverage in their insurance plan will have to start doing so.
While churches, synagogues, mosques, temples and some religiously-affiliated elementary and secondary schools remain exempt from the guidelines, Catholic hospitals, colleges and social services and other Christian institutions are subject to the decision.
"Being a practicing Catholic, I am against that," said Catholic parishioner Robin Cikora. "I believe that there should be a separation of religious and state institutions."
Still, the rule change backed by the White House is supported by birth control and pro-choice advocates like Planned Parenthood of Illinois. President and CEO Carole Brite says religious freedom should not trump basic preventative healthcare.
"There are studies that show for every dollar invested in family planning, nearly $4 are saved in Medicaid costs in the first year alone," said Brite.
However, Catholicism considers some forms of contraception as the termination of life. So some Catholic clergy in Chicago and elsewhere read various letters of protest at Sunday mass.
A letter posted on the Diocese of Joliet website blasted the mandate as "the first time in our history that the federal government is forcing religious people and groups to ante up for services that violate their consciences."
Some legal experts say critics will challenge the constitutionality of the decision.
"Ultimately, I think the Obama administration will prevail on this one again on the theory that [the] health insurance industry is heavily regulated, and if you want to be in the business, you have to make available certain services," said Harold Krent, Dean of the Chicago-Kent College of Law.
The National Association of Evangelicals also opposes the decision. Earlier this month, religious institutions were given a year extension to comply with the Obama administration's decision.
Catholic Church leaders have asked parishioners to unite against the rule and "pray" for a reversal.