Habas is coaching Atletico de Kolkata, owned by La Liga giants Atletico Madid, and reportedly attacked Pires in the tunnel during halftime of the ill-tempered match against FC Goa.
Former Brazilian great Zico, who coach FC Goa, told reporters after the match: "One of our players said that he was beaten by the coach of the other team.
"Pires said he was punched on the face by the Atletico coach and it is very shameful. I am telling you what my players told me and I didn't see that myself but I don't think that Pires will lie and say something that didn't happen."
An ISL spokesperson told Reuters that both teams had written to the League about the incident.
"Both teams have written to the ISL and the incident has been referred to the regulatory commissioner," an ISL spokesperson told Reuters.