After the mutiny the authority tried to investigate this matter. About 70 soldiers died in custody, where the army officers were controlling the interrogation process. At that time government tried to say that it was natural death. But there was allegation that the army is actually taking revenge.
Whistleblower site WikiLeaks recently leaked some cables, which suggest that the junior army officers used aggressive interrogation techniques which caused these deaths. In fact no soldiers died under DGFI interrogation. Those junior officers were used to speed up the interrogation process. Then US ambassador in Dhaka sent cable where he wrote that even Bangladeshi prime minister believes that something is wrong in the interrogation process. The prime minister also believed that there may be Islamic militant involvement in this mutiny.
Many human rights organizations expressed their concern over the custodial death issue and demanded proper investigation that time. The BDR was dismantled after the mutiny and a new border guard BGB was formed by recruiting those soldiers who were not involved in that mutiny.