While many of the groups signing the letter do not get money from the agency, they say the language of the provision is so broad it will affect other, unrelated sources of federal grants. World Vision, for example, received more than $300 million in cash, goods and services from federal sources last year, while the Salvation Army received almost $400 million from federal, state and local governments.

Nathan Diament, director of public policy at the Union of Orthodox Jewish Congregations of America, said that although there are few, if any, Orthodox synagogues or schools that run programs financed by the agency, “the issue for all of our institutions is the broader issue of their continued ability under the Constitution and the Civil Rights Act to be able to hire staff that are consistent with their faith and tenets.”

The debate over federal financing of programs operated by nonprofits with religious affiliations  or so-called charitable choice  dates back to the Clinton administration, when it became part of a welfare overhaul. Organizations are not allowed to discriminate against clients based on religion or require, say, attendance at church services as part of service delivery but are able to exercise their religious beliefs in hiring and other aspects of their operations.

The Coalition Against Religious Discrimination, whose members include the American Civil Liberties Union, the Hindu American Foundation and the N.A.A.C.P., has been pushing Congress to eliminate charitable choice altogether for many years, and it said the pending bill did not go far enough.