"He had not committed any crime, but was sent home for violating public order," Arif Hazarin Sutoto, head of supervision and control at Bogor Immigration Office, told the Jakarta Globe.
The man had reportedly been grieving after the death of his parents and had arrived in the conservative, Muslim-majority nation on July 11 on a tourist visa.
"His visa doesn't [expire] until July 30. But we're going to send him home early," Sutoto said.
The man is understood to have spent time in Bali before travelling to Bogor and reportedly wanted to study at the Dhamma Java Vipassana Meditation Centre in Gunung Geulis.
The security guards who found the man took him to the local police station, Syarief Hidaya, a Bogor police spokesman told the Jakarta Globe.
"So based on the relevant information, he entered the botanical garden last night illegally without buying a ticket by jumping over the fence next to Bhinneka Park."
During his police interview, "JCC" allegedly said he jumped the fence about 10pm on Monday so he could meditate under a tree.
He reportedly told police he heard voices in his head telling him he would be able to fly if he took off all his clothes, so stripped naked and started meditating then climbed the tree and jumped off to try to fly.
He is believed to have knocked himself out after falling.
Hidaya said a urine test found no trace of drugs or alcohol in his blood.
"We suspect the man might be suffering from a mental disorder."
