The incident came to light after a video surfaced on social media.
Both the accused and victim are from West Bengal and the accused is absconding, police said.
Speaking to ANI, Union Minister Kiren Rijiju said, "This incident is really very saddening. We would send a direction to all training centers of Sports Authority of India (SAI) and all the sports institutes in states that there should be a sensitisation programme for all the administrators and coaches."
Rijiju further said, "The role of a coach is essential for any athlete. When a coach teaches a youth then all of us including the parents of the youth trust that coach. If incidents like this happen, then how will the parents trust a coach?
"In all field of sports, we will keep a vigil and try to ensure that these types of incidents do not occur in the future," he said.
Earlier today, the Goa Swimming Association terminated the contract of Ganguly for allegedly molesting the minor girl.
Goa Sports Minister Manohar Ajgaonkar had earlier said, "A criminal action should be taken against the accused Surajit Ganguly."
Taking to Twitter, Rijiju had said, "I have taken a strong view of the incident. The Goa Swimming Association has terminated the contract of coach Surajit Ganguly. I am asking the Swimming Federation of India to ensure that this coach is not employed anywhere in India. This applies to all Federations and disciplines."
Notably, Ganguly had won 12 medals in international swimming competitions with the first coming at the Asian Swimming Championships in Hong Kong in 1984. (ANI)