Krishna Singh, son of a BSF trooper, went missing on Wednesday after visiting a Durga Puja marquees with his elder brother in a BSF campus at Prahari Nagar in Tura in the western part of Meghalaya.
When the boy's family and BSF personnel launched a hunt, the body was discovered with multiple injuries in the campus on Thursday morning.
"It is a gruesome murder and we are suspecting it to be a case of human sacrifice," Meghalaya police chief N. Ramachandran told IANS.
He said two BSF troopers -- Chandrawan and Babu Khan -- had been detained and were being interrogated.
Police have also gone to Mankachar in Assam to quiz Lukman Haqib, a tantrik priest in connection with the murder.