At Gutsa, Lhundup Ganden and three other detainees were stripped naked, beaten with electric batons, and subjected to severe torture during interrogation. After two months, he was transferred to Drapchi Prison and later to Outridu Detention Centre. At Outridu, he spent 34 days in solitary confinement with his hands constantly chained. During this period, he was forced to perform hard labour, held in extremely unsanitary conditions, and exposed to severe cold.

As a result of repeated beatings and prolonged torture, Lhundup Ganden suffered serious head injuries that caused chronic, lifelong headaches. His condition deteriorated further, and he eventually became paralysed from the waist down. In 1990, while still in detention, his sentence was extended to a total of nine and a half years’ imprisonment, along with an additional three years’ deprivation of political rights, on charges of “organising a jailbreak” and forming an independence group.