The proposals will see any group that works with children for more than six hours a week forced to sign up to a new register to counter extremism.
They've been criticised by many as state regulation of the Church.
Addressing the issue in Parliament on Wednesday, Caroline Spelman, who represents the Church Commissioners, said: "Representatives of the Church of England have taken part in detailed consultations with the Government over the proposals to regulate out of school settings.
"I recently led a delegation of backbenchers at the Cabinet Office.
"We understand that this policy remains under review and I'm hopeful that something will emerge which meets the key concerns that those of us have voiced."
The government wants to ensure that young people are not subject to extremist teachings.
But Christian charities CARE, Christian Concern, Evangelical Alliance, Lawyers' Christian Fellowship and The Christian Institute are unhappy at how churches are being targeted.
In a statement, they said: "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 six 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 government recently held a consultation on the plans but is thought to be pushing ahead despite the criticism.
Caroline Spelman addressed a number of other issues raised by colleagues during the session in the House of Commons.
She defended the right of bishops in the House of Lords to take part in debates and votes relating to Scotland.
SNP MP Alan Brown suggested they shouldn't be participating on legislation that doesn't affect them.
The need for more female bishops was also raised by Labour MP Barry Sheerman.
He said: "I want to fill the churches and one of the ways to do that is to have women bishops.
"There are still some very good women who haven't been promoted yet."
Caroline Spelman said 45-per-cent of appointments since the change in law had been women.