Justices Abhay Oka and A S Chandurkar said that the government had failed to file a proper application seeking the High Court's approval for implementing the fare hike.
The Judges also said that there was no urgency in the matter.
The State officials had on June 20 decided on auto fare hike of Rs 2 from the current rate of Rs 15 and Rs 11.33 increase for every subsequent kilometre, up from the current Rs 9.87.
The High Court today asked why the government had not filed proper application even though it had decided to hike the fare on June 20. The Judges said that the application was not in the specified format and advised the state to do so.
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"You (government) took the decision on June 20. Still you didn't file application till July 4. You knew you had to seek HC approval before implementing the fare hike," remarked justice Oka.
Tne Government had filed the application only on July 4 seeking High Court approval for fare hike.
Apart from the government, Mumbai Rickshawmen's Union had also moved the High Court seeking implementation of the fare hike as proposed by the Hakim Committee on the ground that its members are finding it difficult to sustain themselves.
Their contention is that the price of compressed natural gas has gone up from Rs 33.05 to Rs 38.95 a litre, since the last fare hike in October 2012. This has been coupled with hike in the cost of living as well maintenance of vehicles, their application said.