Judges SC Dharmadhikari and Bharati Dangre were hearing a petition seeking court-monitored investigations into the killing of rationalists Govind Pansare and Narendra Dabholkar.
"There is no respect for liberal values and opinions. People are increasingly being targeted for their liberal principles. Not just thinkers, but any person or organisation that believes in liberal principles can be targeted. It's like if there is some opposition to me, I must have that person eliminated (sic)," the court said.
"This trend of killing all opposition is dangerous. This is giving a bad reputation to the country," the court said.
The CBI and the Maharashtra Crime Investigation Department submitted their probe reports in the Mr Dabholkar and Mr Pansare murders. Their progress made by the authorities so far had failed to yield any concrete results.
"While your (probe agencies') efforts are genuine, the fact remains that the prime accused are still absconding. And between every adjournment in the case, one more precious life is being lost," the bench said.
"One more precious life was lost last month when in an unfortunate incident, a liberal, like-minded person was killed in Bengaluru," the court pointed out.
"What's the guarantee that more people will not be targeted for their beliefs and principles in the future? If the accused persons and organisations are feeling emboldened, then the probe agencies should take that as a challenge," the bench said.
The court was referring to the fact that Sarang Akolkar and Vinay Pawar, the two men suspected by the CBI in the Dabholkar killing in 2013, are yet to be traced.
The court dismissed the apprehension expressed by the families of Mr Dabholkar and Mr Pansare that the agencies were not probing the role of right wing group Sanatan Sanstha in the killings.
"While the court can't make details of the probe public, we can say this much that the probe reports have examined all angles. They have not ignored the possibility of the role of Sanatan Sanstha in the case," the bench said.
Mr Dabholkar was shot dead on August 20, 2013, in Pune while he was on his morning walk. Mr Pansare was shot at on February 16, 2015 in Kolhapur.
(With Inputs From PTI)