The proposed changes could reduce the period someone has to have lived in their new gender from two years to six months, with three of those as a cooling off period before the finalisation of the gender change.
The Scottish Government have committed to a further period of consultation though, before bringing the legislation to the Scottish Parliament.
In that consultation the proposals will also consider reducing the age requirement for gender change from 18 to 16.
The Evangelical Alliance, a body of Christians and churches across the UK, said: "The continued push to allow a child to self-identify is deeply concerning.
It added that it wanted "to encourage the church and wider society to respond with compassion to those wrestling with gender dysphoria; to seek clarity that is not based on ideology; and to create space for concerns around the rush to invasive procedures and safeguarding single-sex spaces."
The alliance also said it was "encouraged that the government have listened to some of the concerns raised and will continue to engage with the proposals to be published in a draft bill".
Kieran Turner, public policy officer for Evangelical Alliance Scotland, said: "Today's announcement paints a mixed picture. We welcome the new consultation and the fact that the Scottish Government have recognised the need to reflect further in light of the many concerns about this legislation. We also welcome the review of youth guidance and the commitment to retain the existing protections of the Equality Act.
"However, in other areas the government are still looking to press ahead, even if, at a slower pace. While the Scottish Government want to move away from language of self-identification, that is still ultimately what is being proposed. Sadly, the government have failed to take the opportunity to clarify that under 18s will not be able to self-identify. We will continue to engage with the Scottish Government on this issue, providing a clear and compassionate Christian response."
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