"The sentiments expressed by the protesters were the result of extreme provocation and the state was with them in this hour of grief," he said.
"My sentiments have also been deeply outraged by the desecration and I can understand the actions of the people", he said.
The Deputy CM, who also holds the Home portfolio, said he had directed Punjab police to withdraw all cases registered against protesters at both Kotkapura and Behbal Kalan, both in Faridkot district, as well as anywhere else in the state.
Badal also appealed to Punjabis to maintain peace and communal harmony at all costs.
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"There are some forces who would like to disturb the peace in Punjab. We must not let such people succeed in their nefarious designs," he said.
He also assured the people that the Punjab government was with them in their hour of grief and was taking steps to arrest the culprits responsible for this "ghastly crime" immediately.
Police have booked close to 500 people under various sections of the IPC in connection with the clashes.