Special CBI Judge Sanjeev Aggarwal, however, acquitted two other accused in the case - Lhakpa Tsering and Krishna, who were facing trial in this case along with Thungon, then Urban Affairs and Employment Minister Sheila Kaul, and one Tulsi Balodi.
Proceedings against Kaul and Balodi were abated after the court was informed that they died during the pendency of trial.
The court, which will hear arguments on sentence tomorrow, held Thungon, also ex-Chief Minister of Arunachal Pradesh, guilty of offences under section 120B (criminal conspiracy) of IPC read with sections 13d(iii)(if while holding office as a public servant, obtains for any person any valuable thing or pecuniary advantage without any public interest) and other provisions of Prevention of Corruption Act.
A case was registered by the CBI in 1996 against Kaul, Thungon, Tsering, Krishna and Balodi for allegedly hatching a conspiracy in allotting shops and stalls in 1994.
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offence of criminal breach of trust to cause undue pecuniary advantage to their relations and friends, Tsering, Krishna and Balodi and dishonestly allowed these three to convert to their own the government shops entrusted to the minister.
It had said that in pursuance to conspiracy, Kaul abused her official position as Minister and in the capacity of custodian of government shops, dishonestly and without any public interest sanctioned allotments of three shops without calling for any tenders of applications from general public on mere recommendation of Thungon in a market opposite Red Fort.
CBI said the case was registered after the Supreme Court in 1996 directed the agency to probe the allegations of corruption and bribery in the matter of out-of-turn allotment of government shops and lodge cases against the offenders.
The three shops were alloted on April 9, 1994 and May 12, 1994, the agency had said.
The court had framed charges against the accused in March 2009 for the offences of criminal conspiracy read with criminal beach of trust by public servant of the IPC and under relevant provisions of the Prevention of Corruption Act.