Senomen S Marak (19), accused of stealing a bike, allegedly hanged himself inside the lock-up, a day after villagers handed him over to police.
Marak was caught in Jaksongram in South Garo Hills along the Indo-Bangla border. He hailed from Rongdok in West Khasi Hills district.
Warjri also said the state government would soon install Close Circuit Televisions (CCTVs) in all police lock-ups across the state to prevent a repeat of such an incident.
"I have asked the police department to immediately expedite the process for installation of CCTVs in all police lock-ups," Warjri said.
Twelve persons have died in police custody in the state in the past five years. Three custodial deaths have been reported in the state this year.