Dozens of people started pelting stones at security forces during the operation in Pinjoora area of Shopian district this morning, a police official said.
He said police used tear gas shells and batons to chase away the protestors.
The security forces had launched the operation after receiving information about presence of militants in the area but the searches were called off as no suspicious person was found there, the official said.
There were no reports of anyone getting hurt during the brief clashes, he added.