The navy said in a statement Tuesday that the Indian submarine wasn't targeted, "keeping in view Pakistan's policy of peace" under which Islamabad wants to de-escalate tensions with New Delhi.
A navy official says the warning was "communicated" to the submarine during Monday's encounter. The submarine then moved away. He didn't elaborate and spoke on condition of anonymity to talk to reporters.
Tension escalated after India last week launched an airstrike inside Pakistan, claiming it targeted militants behind a Feb. 14 bombing in Indian-controlled Kashmir that killed 40 Indian troops.
Pakistan retaliated by downing two Indian fighter jets and capturing a pilot who was later handed back.