Naval Chief Admiral Nirmal Verma indicated that the matter had been taken up with the international coalition of naval forces operating against piracy.
He said PNS Babur, while escorting Egyptian merchant vessel MV Suez which had been released by Somali pirates, brushed off the Indian ship after moving close as it was coming from behind.
"Our ship was going at a particular speed and the other ship approached from the rear as it must have tried to pass at a certain distance... but it didn't happen as it turned up very close," Verma told reporters after the incident that occurred last week.
"We operate helicopters from ships and we keep the helicopter nets down (during landings). One of our helicopter nets got damaged," he said.
The Naval chief said INS Godavari had been sent to reassure the Indian sailors on board the MV Suez after its release from captivity of Somali pirates.
"After that this incident took place where the Pakistani Navy ship came much closer than what is considered to be prudent by anybody operating ships in the seas," he said.
Asked if the multi-national Combined Task Force 151, under whose command the PNS Babar was operating, had been informed about the incident, Verma said, "You can be sure that everybody knows about that."
India has already lodged a protest with Pakistan over the incident and provided photographic evidence about the dangerous manoeuvres by PNS Babur.