The "stop work" order on Tzu Chi Foundation's new national headquarters complex was placed last week near San Dimas.
Neighbors complain that as many as 10 oak trees were removed from Walnut Creek County Park without permission, and construction activities extended well into the night.
Tzu Chi Foundation spokesman Robert Hsu says the Buddhist group is seeking the necessary permits.
County officials say the foundation will have to replace the fallen oaks or pay to replace them.