A bench comprising Justices BR Gavai and PS Narasimha was hearing a plea filed by the Jamiat Ulama-i-Hind, in which the organisation alleged that authorities were specifically targeting the Muslim community.
The court also said that it will hear the organisation's plea against demolitions on 10 August, news agency PTI reported.
"Rule of law has to be followed, there is no dispute on that. But can we pass an omnibus order? If we pass such an omnibus order, will we not prevent the authorities from taking action against the violators," the bench remarked.
The apex court had issued a notice to the Uttar Pradesh government following demolitions in the state. In its reply, the government stated that such demolition drives were lawful and routine to remove allegedly illegal encroachments.
On 12 June, the UP administration had demolished the property of Javed Mohammad, an activist associated with the Welfare Party of India.
Javed was accused of being the main conspirator of the violent protests that erupted in UP's Prayagraj over the remarks of suspended Bharatiya Janata Party (BJP) Spokesperson Nupur Sharma against Prophet Muhammad.
The activist was taken into custody by the UP Police on 10 June, along with his wife Parveen and daughter Sumaiya.
Demolitions were also carried out in Kanpur in the aftermath of the violent protests in UP.