"We have witnessed Pakistan indulging in false propaganda and spread of misinformation. The Indian Navy does not take cognizance of such propaganda. Our deployments remain undeterred," the Indian Navy said.
In a brief statement, it said the Indian Navy remains deployed as necessary to protect national maritime interests.
The claim by Pakistan Navy came in the midst of the latest flare-up between the two nuclear-armed neighbours.
"The Indian submarine was not targeted keeping in view Pakistan's policy of peace," the official said, adding that India must learn from this incident and "move towards peace".
"The Pakistan Navy is always ready to guard its territorial waters and is capable of responding to any kind of aggression with full force," he said.
The next day, Pakistan Air Force tried to target Indian military installation in Kashmir but was thwarted by the IAF which lost a MiG-21 while its pilot Wing Commander Abhinandan Varthaman was captured. He was handed over to India on Friday.