A division bench of Justices D Y Chandrachud and Amjad Sayed was hearing a public interest litigation filed by an NGO challenging the fare hike.
The deadline set for recalibration has to be extended from time to time and it is now February 2013.
The state government told the court that there are only three agencies in the city that can recalibrate electronic and mechanical meters.
On an average, these agencies can calibrate 2000 meters in a month, while there are 60,000 autos and 16,000 taxis yet to be recalibrate, the court was informed.
The bench was also informed that the three agencies are in suburban Bandra and Kandivali and at Byculla in South Mumbai.
The Byculla centre is inaccessible for autos as they are not allowed to ply in South Mumbai.
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"Evidently, a failure in planning process is there, which needs to be rectified at the earliest," the court said, directing the government to come up with a plan of action on how the problem would be sorted out.
The court has also asked the government to consider appointing three agencies in the east region and three in the west to speed up the process.
The matter has been posted for further hearing on December 20.