The case was registered yesterday after several people alleged that the army personnel thrashed them and snatched away their money, the sources said.
The FIR has been registered under Sections 392 (robbery), 341 (wrongful restraint) and 323 (voluntarily causing hurt) of the Ranbir Penal Code.
At least 10 persons, including two employees of the Department of Animal Husbandry, were injured in the incident, the sources said.
The Army, however, has denied involvement of any of its personnel in the incident.
"Our troops were not involved in the incident...We are investigating who the culprits are," an army official said.
Srinagar-based defence PRO Lt Colonel J S Brar said he was not aware of any such incident.