Under Toomey's plan, exemptions from the ban would cover organizations managed by a church or religious group, those formally affiliated with a particular religion, or those that teach a curriculum directed toward propagating a particular religion.
His amendment specifies that the exemption includes groups that don't primarily engage in religious work - for example, a school that teaches religion only a few hours a week, or a hospital affiliated with a religious group.
Under existing law and the ENDA proposal, exceptions are only for institutions whose "purpose and character are primarily religious." (Civil rights laws let faith groups use preferential treatment in hiring people of the same religion but bar preferences based on factors such as race, gender, or other factors.)
Toomey worried that the ENDA language on faith groups was vague and open to court interpretation. "Different circuit courts have come to different conclusions," he said Tuesday. "There's a lot of uncertainty and inconsistency."
While he voted to advance the bill Monday, he has not committed to supporting its final passage.
He was one of seven Republicans to vote to open debate on the bill, a top priority for gay-rights groups for years.
A Toomey statement Monday said he has "long believed that more legal protections are appropriate to prevent employment discrimination based on sexual orientation" but that "we must strive to reach the appropriate balance between protecting workers and protecting religious freedom."
While his plan will get a vote, Senate ENDA sponsors were noncommittal about supporting it. They were more open to an amendment from Sens. Kelly Ayotte (R., N.H.) and Rob Portman (R., Ohio), which will need only 50 votes for approval.
Conservative groups have argued that ENDA could impose government values on business and interfere with faith groups. But gay-rights advocates had pressed Toomey to back the bill.
Levana Layendecker, a spokeswoman for Equality PA, said, "We would be more than willing to hear Sen. Toomey's concerns and work together to make sure his concerns are addressed."
Toomey's vote won hearty praise from State Rep. Brian Sims (D., Phila.), an openly gay lawmaker who said in a news release that it showed "a conservative ideology and support for LGBT equality are not mutually exclusive."
While the bill likely faces a dead end in the Republican-controlled House, the Senate vote was seen as the latest sign of the political sea change on gay rights.
For Toomey, who has built his political career by focusing on fiscal issues, the vote was a second prominent example of his move toward the center on a highly charged cultural issue. In the spring he cosponsored a plan to expand background checks on gun buyers, also winning praise from moderates and Democrats.