The singer set up the Awen Project with her husband Jonathan Powell in 2019 to “tranform education” for children and let them “follow their passions”.
Children at the school learn as part of a “large network of Tribes” where they are taught to “become healthy, informed, and responsible members of the global society”.
Pictures on the school’s website showed children being taught in the woodlands under a large tent and in another image are doing homework while sat around a camp fire.
However, the Woodland Trust said it has “sadly” taken the decision due to multiple breaches of health and safety by the Awen Project, which the Welsh singer set up in 2019.
The charity, described as supporting “learning communities” at temporary structures in woodlands, had been operating at woods located between the village of Michaelston-le-Pit and the town of Dinas Powys in South Wales.
Ms Church has launched an appeal to find a new location for her project, saying the news had been a “rollercoaster”.
A Woodland Trust spokesman said: “Sadly, and after much deliberation, we have taken the decision to terminate the current permission granted to the Awen Project for their use of Cwm George & Casehill Woods.
“This is due to multiple breaches of this permission, which have posed health and safety concerns for our visitors and wildlife within the ancient woodland.
“We have, however, offered a new Forest Schools licence which sets out a new arrangement going forward that is in keeping with the fact that Cwm George is a publicly accessible woodland, managed for people and wildlife.”
In a statement posted to Instagram on Friday, Church wrote that the Awen Project was in “desperate need” of a new home to host the charity’s work.
She added: “Despite our best efforts to salvage an effective and mutually beneficial partnership with woodlandtrust, unfortunately they have revoked our license agreement, meaning that we can no longer deliver our outcomes for the children and families that we support or keep striving to change how we access excellent education for all children.
“It has been a rollercoaster - and we tried so hard to stay where we were - but as a very small charity we just couldn’t keep going against the big guys.
“If you have any land in Barry, Dinas, Penarth, Cardiff or the general South Wales area, please reach out to them directly.
“Alternatively, if you have any advice, suggestions or solutions they’d love to hear from you too. You can also donate via their website to aid with them finding a new home. Thank you.”
The Awen Project has been contacted for comment.
Additional reporting by PA