Mehra said that health department team searched the Shah Satnam Speciality Hospital inside Dera HQ premise and sealed the skin bank which was running without licence.
Irregularities in the implementation of the Medical Termination of Pregnancy (MTP) Act by the Dera were also detected, he said.
Mehra said that SMS, internet and Railway services in Sirsa will resume from tomorrow. As soon as the verdict of the court was announced against Ram Rahim his supporters broke out on the roads torching and burning vehicles and properties protesting against the court's decision.
After Ram Rahim's conviction, a former Dera security officer, in an interview, had alleged that Baba's henchmen used to murder people inside the premises and then bury their skeletons inside the headquarter. The arson and violence left 35 people dead and scores of people injured in Panchkula. Pawar was appointed by the Punjab and Haryana High Court on Tuesday as the Commissioner of the Court for this work.
The police and the dera management have maintained that licenced weapons were deposited by most of the dera followers at Sirsa with the police authorities.
Meanwhile, a case has been registered against the Dera, said Mehra.
Earlier in the day, the search revealed an illegal factory inside the premises. Reportedly the other fibre glass tunnel opened some five kilometre away from the Dera head's private residence.
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The government official also said an unregistered Lexus, demonetised notes, and cash were seized from the Dera headquarters. While it was earlier said that she was living at a followers house it Rohtak, rumours also have it that she could have fled to Nepal.
The search team found a window-like tunnel connecting Ram Rahim's room (Dera Awas) to the room of Sadhvis (Sadhvi Niwas).
Inside the campus, lay luxurious resorts and mini models of Paris' Eiffel Tower, Taj Mahal, Disneyland and even a Khel Gaon (sports village).
Chawla added that the police were still looking for two key Dera Sacha Sauda functionaries - Honeypreet and Aditya Insan.
The entire sanitisation process was videographed.
The operation will continue uninterrupted till the search is complete.
Gurmeet has been convicted of raping at least two of his women followers in 2002 and sentenced to 20 years in jail. The exercise is being conducted amid tight security by police and paramilitary personnel, besides senior officials of various government departments.