The 20 year-old was currently serving a 14-day judicial custody after he and four of his aides were arrested on May 13 for their alleged role in confining twelve young women and torturing them, they said.
Marak was admitted in the hospital on Monday evening after he complained of fever, body ache, pain in the elbow and right ear infections, SP Mukesh Singh said.
The deceased was referred to the district civil hospital on May 17 by the jail medical officer he complained of high fever and ear problem, jail superintendent J J Sangma said.
The mother of the deceased, Mina S Marak, however has alleged foul play in her son's death and has accused the police of torture.
According to her, Marak was innocent and was arrested merely because he was found hanging out with another accused.
"He had no role in the case and had only returned on May 13 from Nongalbibra," she said.
The state government today ordered a high level inquiry into the custodial death of Marak, which would be headed by Garo Hills Division Commissioner P W Ingty.
Ingty was tasked with the responsibility to probe into the circumstances of death through medical and other related evidences, both factual and circumstantial, the government said in a statement issued here adding the Commissioner was given a 30 day-period to submit his report.
The government also appealed to the citizens in Garo Hills to assist the law enforcing agencies and to maintain peace and harmony in the area.