The protected Tshatshingo potholes in Limpopo face an "ecological catastrophe" after several rare flora species were uprooted to make way for a picnic spot.
The potholes are rare natural structures that take hundreds of thousands of years to develop in a river bed.
Deforestation by a developer allegedly caused visible erosion after trees were removed near the potholes.
Department of Tourism and Environmental Affairs spokesman Lehlogonolo Masoga said that protected riparian bio-diversity had been damaged while the developer was busy.
"When we approached the developer, he told us that he was not aware that an Environment Impact Assessment (EIA) had to be conducted. We subsequently stopped construction.
"If he does not comply we will charge him with contravening environment and protection management acts," Masoga said.
The department said the developer has been warned to stop construction until an EIA report has been submitted.
The site in dispute is at Tshidzivhe. It is a few metres from the holes and a small river that supplies water to these holes.
The Tshivhase royal council had agreed to offer land in the area to businessman Josias Munyamela to be developed into a picnic site. The Department of Tourism and Environmental Affairs has threatened to take Munyamela to court if he continues with construction at the spot without an EIA report.