The bizarre incident came to light after the daughter of the woman passenger tweeted about the incident on Friday.
The incident has shocked one and all and has brought the national carrier under stern criticism.
The civil aviation ministry sought a report in the matter from the airline.
Indrani Ghosh, daughter of the woman passenger, tweeted tagging the civil aviation minister Suresh Prabhu and external affairs minister .
“Disgraceful @airindiain yesterday on your flight AI102 from JFK to Delhi a drunk passenger removed his pants and peed on the seat my mother was sitting!!! She was travelling alone and is completely traumatized! Reply ASAP #AirIndia #Shameful," she tweeted.”
Giving details about the alleged incident, Ghosh added, "@airindiain when I called to make a complaint the usual call centre guy following the script asked me to go to the website and write a feedback!! Really FEEDBACK!"
She also demanded strict action against the drunk passenger and said that by "reporting such obscene and offensive behavior the airline can stop such a person from creating nuisance in future".
Air India “strongly” condemned the incident on Saturday and also apologised to the passengers for the inconvenience they faced onboard its aircraft.