"We're clear about not giving them (US doctors) permission to bring Dede to the US," health ministry spokeswoman Lily Sriwahyuni Sulistiyowati was quoted as saying by Warta Kota daily.
"Moreover, people like Dede, who live in small villages, don't want to be taken away, especially to give blood samples. Normally village people don't easily give foreigners permission to test their blood," she said.
The spokeswoman declined to give an immediate comment when contacted by AFP.
Anthony Gaspari, a dermatologist from the University of Maryland, examined Dede as part of the documentary.
He believes the massive growths are a combination of the human papilloma virus, which causes warts, and a genetic disorder that means his immune system is too weak to fight them off.
Gaspari told AFP from the United States that he was disappointed by the reported health ministry decision but said it would not stop his initial plan to treat his condition.
Gaspari said he was in negotiations with a US pharmaceutical company to provide Dede with an ongoing supply of vitamin A, which would hopefully boost his immune system and hinder the growth of the warts.
"My initial plan would be to send medication to Indonesia to a local doctor to administer," he said. "If it doesn't work I won't have any choice but to try to get him over here."
Possible alternative treatments, such as chemotherapy, carried higher risks and needed to be closely monitored outside of Indonesia, Gaspari said.
Genetic testing would also require fresh blood samples, which meant they would have to be taken in the United States, he added.
"I suppose at a university in Indonesia it's maybe possible to do the testing, I just don't know whether the expertise would be available," he said.