The destinations of the cancelled flights were: Port Blair, Mumbai, Agartala, Dibrugarh, Delhi, Bagdogra and Imphal.
However, two flights -- one to Guwahati and the other to London -- had taken off as scheduled, Air India sources said.
Alliance Air has also operated three of its six daily scheduled flights to Shillong, Imphal and Silchar. It is likely that other three will also take off as per schedule, they said.
Countrywide, around 60 Air India flights were cancelled today while several others delayed.
Eight hundred-odd pilots, belonging to the erstwhile Indian Airlines owing allegiance to the Indian Commercial Pilots Association had gone on an indefinite strike from Tuesday midnight.