Police and state welfare authorities in the eastern state of Orissa took the boy, Budhia Singh, for medical tests on Friday after India's human rights watchdog ordered an inquiry into the case.
Budhia gained a place in local records by running 65km on Tuesday from Puri to Bhubaneswar in the eastern Indian state of Orissa.
Pramila Mallick, Orissa's child welfare minister, said: "Budhia Singh will not be allowed to run marathons."
Mallick said a team of doctors who conducted medical tests on the boy found he was undernourished, anaemic and under cardiological stress.
"His health would be adversely affected if he is allowed to run marathons," she said.
Doctors found "blood pressure and urea levels in his body were very high and there was the risk of him developing renal failure if he ran long distances," Mallick said.
Budhia will be allowed to be trained by a coach to hone his talent at an appropriate age, she added.
After receiving complaints from civic groups, India's National Human Rights Commission ordered the Orissa government to conduct a health check on the boy and investigate those who organised the run, saying they believed the child's human rights had been violated.
Officials at the commission in New Delhi declined to comment on Monday, saying they had not yet received the medical report.