The woman was assaulted following an altercation with the woman passenger over change for a Rs 50 note near a petrol pump at New Alipur, Deputy Commissioner of Police (South) Murlidhar said, adding the auto-rickshaw driver was arrested.
This is the second incident within a fortnight.
Earlier on January 16, a woman executive was punched on her face and left bleeding by an auto-rickshaw driver at Park Circus.
With the increasing number of complaints of misbehaviour and overcharging by the auto-rickshaw drivers in the city, the government had announced measures to rein them.
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Transport Minister Madan Mitra had yesterday announced that the government would press non-bailable charges to rein in rouge auto-rickshaw drivers in the city and stop them from overcharging the passengers.
The government has also decided to set up a helpline for the passengers to register their complaints against them.
Mitra today visited a number of areas and said auto-rickshaws were found charging different fares for the same distance.
"Some were charging Rs 9, while others Rs 13 for the same distance," he said.
"The teams will report exactly what is happening in 125 auto routes in the city, how many auto-rickshaws were running in each route and the fare being charged," Mitra said.
Instructions have also been issued not to allow auto-rickshaws on the roads without valid papers, he said.
Mitra said that passengers should call helpline number 1073 in case of problems with auto drivers.