Secret tunnels, including one which linked jailed sect chief Gurmeet Ram Rahim Singh's plush residence with female disciples' hostel, an empty box of AK-47 cartridges, an illegal firecracker factory were among other shocking detections made, according to Haryana's Public Relations Department Deputy Director, Satish Mehra.
Irregularities in the implementation of the Medical Termination of Pregnancy (MTP) Act by the Dera were also detected, he said.
However, curfew will remain in force near Dera Sacha Sauda complex, he said adding that relaxation will be given to the residents to buy daily necessities.
Security agencies and government departments had launched a coordinated effort as part of this exercise which was overseen by a court commissioner.
The sanitisation exercise was conducted two weeks after Dera chief Gurmeet Ram Rahim Singh was convicted and jailed by a special CBI court for raping two disciples.
There was large scale violence following the sect head's conviction which left 35 people dead in Panchkula alone.
Violence broke out in Sirsa, where six died, and many parts of Punjab as well.
"The search operation process in the Dera was launched on September 8 and was overseen by Court Commissioner AKS Pawar. The search operation continued till Sunday and the process is complete now," Mehra told reporters this evening. He said the process remained smooth and peaceful.
Giving details, Mr Mehra said that a health department team searched a hospital running inside the Dera and sealed a skin bank which was allegedly "running without licence".
"Also, it was found that no record of the dead bodies being sent out of the hospital had been maintained," Mr Mehra said.
He also said that a health department team detected irregularities in the implementation of the Medical Termination of Pregnancy (MTP) Act by the Dera.
Besides, an illegal wood cutting machine was sealed and some 'lathis' were also found, he said.
The sanitisation process led to unearthing of two secret tunnels, including one that connected the Dera Sacha Sauda chief's residence with the hostel for female disciples, and an illegal firecracker factory.
The other fibre glass tunnel detected by the security forces opened some five kilometre away from the Dera head's private residence.
Computer hard disk drives, an unregistered Lexus car, an OB van, Rs 7,000 of demonetised currency, Rs 12,000 cash and some pharma medicines without labels or a brand name, a walkie-talkie set were also seized, the official said.
Mr Mehra said forensic teams were also involved in the sanitisation exercise.
During the sanitisation operation inside the Dera, the authorities also found five boys, two of them minor, from Upkar Colony, where some Dera followers permanently reside, he said.
"The search operation process is 100 per cent complete now. Officials in charge of various sectors made for the purpose of search have submitted their report to the Court Commissioner AKS Pawar who has to submit the report to the Punjab and Haryana High Court, Mehra said.
The Dera's sprawling headquarters include a township of its own, with schools, a sports village, a hospital, a shopping mall and a cinema hall. The property is also home to an ostentatious '7-star MSG resort' with replicas of Eiffel Tower, Taj Mahal, Kremlin and Disney World inside.
Police, paramilitary and civil administration personnel were involved in the mammoth operation which started on Friday on the direction of Punjab and Haryana High Court.
The entire sanitisation process was videographed.
The Dera headquarters, spread over nearly 800 acres, was divided into ten zones for the purpose of sanitisation and searches, with each zone under the control of a senior officer.
The Dera chief, who featured in a few films directed and co-produced by himself, also has some shops in the complex where consumer products launched two years ago under "MSG" brand were sold.
Quick Reaction Team vehicles, heavy earth moving machines, bomb disposal squad, anti-sabotage team vehicles, dog squads, tractor trollies and fire tenders were pressed into service in the mammoth exercise.
The Dera management had said it would cooperate with the authorities.