"Why is the government avoiding a judicial inquiry into the riots? One-sided action by the administration will not be tolerated," senior BJP leader Rajnath Singh told reporters in Kosi Kalan.
"If the administration is found to be at fault, then action should be taken against it," he said.
Accompanied by Uttar Pradesh BJP chief Laxmi Kant Bajpai, Singh interacted with victims of the riots.
Four persons were killed and 16 others injured after communal clashes broke out in Kosi Kalan, about 45 km from Mathura, on June 1, reportedly after a pedestrian used water meant for some religious purpose.
On BJP's choice for the President's post, Singh said the party would decide once the Congress "opens its cards".