Home side Goa led 1-0 at half-time of the Indian Super League clash on Thursday thanks to Andre Santos' strike, before the visitors came back in the second period as Cavin Lobo's brace sealed a 2-1 victory.
After a fractious affair that saw seven players cautioned, it was alleged that Lopez had struck former World Cup winner Pires as the players left the field at the break.
"The other thing that happened which is more serious is that one of our players said that he was beaten by the coach of the other team," Zico said.
"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."
Kolkata team owner Utsav Parekh has announced his team's intention to contact the ISL, in order to clarify the situation.
"Look, none of us was present on the spot when the alleged incident took place," he told The Telegraph in India.
"We are writing to the ISL about it and we expect them to investigate the matter and come out with the truth.
"CCTV footage is available and so it will not be very difficult to establish the truth. Whatever the incident, one can find that out from the CCTV footage."