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SAN ANTONIO -- From their quiet cubicles, employees with San Antonio's Catholic Charities help refugees from Iraq, who are escaping that war-torn region for the United States. Phone calls provide immigration attorneys and a place to stay for the refugees.

It takes federal dollars to fund some of the resettlement work, and Catholic Charities is listed as a government contractor.

And that status may now be under fire.

"We understand the legislation could have a deep impact on our organization. However, until we get more information from the Archdiocese, we are unable to make a comment at this time," said Catholic Charities of San Antonio spokesperson Patricia Vela.

With the stroke of a pen, President Obama signed an executive order last week, banning federal contractors from discriminating against homosexual and transgender employees. The White House calls it "progress."

Religious groups are worried because President Obama didn't include and protections for faith-based organizations--many of which hold conservative views on sexual orientation and also receive some government contracts to help the poor and marginalized of society.

"That would impact us in that respect," said Vela.

It's estimated some 40 percent of San Antonio's Catholic Charities work is supported by federal monies. Other religious groups, like the Salvation Army, have similar federal contracts, providing assistance and expertise with refugees, the orphaned and the homeless.

Local canon lawyer Michael Dunnigan says President Obama's order may discourage these faith-based agencies from seeking government dollars altogether.

"It's abandonment of the poor, because again, you're taking out of the equation the organizations that have proven to be very effective and very efficient at delivering these services. And it's also an assault on people of faith," said Dunnigan.

In a statement to the I-Team, a spokeswoman for the Salvation Army's National Headquarters said, "We have recently received the order and are currently reviewing the context."

A spokeswoman for the President of the United States Catholic Conference of Bishops put it bluntly, telling the National Catholic Register "If you hold that certain sexual practices are immoral, there is a good chance you probably will be disqualified from contracts."

The executive order takes effect immediately, and attorney Dunnigan said so does its chilling effect on religious non-profits.

"The faith is more than just worship. The faith is about going into the world and helping other people, whether they're Catholic or not. That's not just a key part not just of Catholicism, but of many religions," said Dunnigan.

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