"We encourage you to keep admiring, appreciating, and loving on our amazing Joshua trees -from the ground."
Meanwhile a spokesperson for the national park called her out via the Desert Sun.
"We would just remind [Cyrus] that she has a big following, people watch what she does, and it would be greatly appreciated by the Park Service and the people around the area if she would maybe curb that type of activity, especially posting it on her social media page."
Attaching hammocks, slack lines or other ropes between the trees in Joshua Tree is prohibited.
The Malibu singer is yet to respond to the backlash.
As of Thursday morning the images were still on her Instagram page, although she did turn off comments.
Concern about the future of the Joshua tree is valid. The US Fish and Wildlife Service is investigating research indicating the species could be wiped out by climate change.
As global temperatures rise, scientists have found the trees have stopped reproducing in hotter and drier areas in the region.
Joshua Tree was vandalised during the US government shutdown in January, when most workers were sent home unpaid. A protected Joshua tree was cut down at its base.