It's not yet clear if the policy will affect the airline's international routes.
The state-owned airline will also keep plastic handcuffs on all flights to restrain passengers who are "out of control".
"We feel, as national carriers, it is our responsibility to enhance comfort level to female passengers," Air India's Meenakshi Malik told The Hindu. "There are a lot of female passengers who travel alone with us and we will be blocking a few seats for them."
It's not uncommon for women and men to travel separately in India, with many long-distance trains and buses reserving sections for women.
However, it's sure to ruffle a few feathers. Former executive director Jitendra Bhargava told The Hindu the move was unnecessary, calling it a "misplaced priority".
This isn't the first time Air India's gender equality credentials have been called into question. In 2015 the airline was criticised for announcing plans to ground 125 mostly female flight crew for failing to meet the company's body-weight standards.