Plans to register and possibly inspect Sunday schools are still in place and threaten churches, the Evangelical Alliance has warned.
In a statement marking a year since the government consultation closed, the evangelical umbrella body warned that the programme to monitor what Sunday schools teach is still under consideration.
Education minister Lord Nash confirmed the government is "committed to regulating out-of-school settings" at questions in the House of Lords on Wednesday afternoon.
"We want a system that regulates out-of-school settings and works effectively but is not overly burdensome, because we know that many of these settings are small and staffed by volunteers," he told peers.
The suggestion in place would force any setting that educates children for more than six hours a week to register with the government. This would include a number of Sunday schools and church youth groups.
Ofsted inspectors would then be allowed to check on what was taught if a complaint was made.
Opponents say this leaves churches open to vexatious complaints if they teach against gay-marriage.
Simon McCrossan, head of public policy at the Evangelical Alliance, said this showed religious freedom was "an after-thought at best" in Theresa May's government.
"These plans could lead the way to a register of Sunday schools, and making the government the arbiter of what doctrine is or isn't desirable," he said.
"Instead the government need to ensure freedom of religion is at the heart of their plans because it is a key British value. It is currently an after-thought at best.
"Theresa May said this week: 'When the state intervenes it intervenes effectively, it intervenes when it is right for the state to intervene.' We call on the prime minister to heed her own words and acknowledge it is neither right for the government to intervene to regulate Sunday schools, nor effective to do so."
The comments come after Dame Louise Casey, the government advisor on integration, told MPs "it is not okay" for church schools to teach marriage is between one man and one woman.
Church schools cannot be "anti-gay marriage" she said in a select committee hearing and warned such a view was "often veiled as religious conservatism" but in reality was "homophobic".
McCrossan said: "Dame Louise Casey appears to conflate legitimate concerns about safeguarding and terrorism with trying to enforce new social norms on church schools.
"We won't tackle terrorism and violent extremism by stamping out religious freedom, we can't have school inspectors becoming regulators of peaceful religious doctrine."