The Lawyer's Christian Fellowship, CARE, the Evangelical Alliance, the Christian Institute and Christian Concern all contributed to the statement, which refers to plans to monitor any church which provides six or more hours of teaching to children every week.
The proposals would also see churches put on a national register.
The government did conduct a consultation on its proposals, however it has been criticised because it was held over the Christmas period - the busiest time of the year for many Christians.
In a statement, the group says: "Requiring churches in England to register before they are legally allowed to help children learn the Christian values our nation was built on is an unjustified restriction of religious liberty.
"Whether the threshold is 6 hours in any week or higher, the principle of outlawing 'unregistered churches' from teaching children the gospel is an unacceptable overreach of the state."
The group is calling for the government to use a targeted, intelligence-led approach to tackling extremism in Britain rather than the current proposals.
Mark Jones, the Chairman of the the Lawyer's Christian Fellowship, told Premier's News Hour: "Six hours can be made up in a number of different ways, if a church has a weekend away that'll be certainty more than six hours in a week, it's not an average period, it can be any week at all.
"They would need to register, I imagine most churches would register, those who are aware of the law, if they don't register then there are potential sanctions.
"There are individuals who could be prevented from teaching and... an organisation could ultimately be closed down."
"If what is put into place is what is currently proposed, the idea of compulsory registration for any organisation that engages children in activities for over six hours, then that is something that would be open to challenge."
A Department of Education spokesman said: "We recognise that many out-of-school education settings do a great job in supporting children's education - but nothing is more important than protecting children from intolerant and hateful views.
"This Government is not proposing to regulate institutions teaching children for a short period every week, such as Sunday schools or the Scouts. Nor will it apply to one off residential activities, such as a week long summer camp.
"We consulted on our plans and received a large number of responses which we are now considering and will make a further announcement in due course."
Listen to Premier's Aaron James speaking to Mark Jones on the News Hour:
