The Indian fisherman was killed in the firing by Pakistan Maritime Security Agency.
India has taken "serious note" of an incident in which the Pakistan Maritime Security Agency, in an "unprovoked" firing incident, opened fire at an Indian fishing boat resulting in the death of one Indian fisherman and another injured.
The injured fisherman is being treated at a hospital in Okha, Gujarat, sources said.
The Indian government will "take up" the issue diplomatically with the Pakistan side.
"The matter is under investigation and further details will be shared in due course," a source said.
Reports from Maharashtra said a 32-year-old fisherman from Maharashtra was killed.
The incident occurred around 4 pm on Saturday.
A fisherman from Thane near Mumbai, who was on a fishing boat, 'Jalpari,' was killed after the Pakistani Maritime personnel opened fire on him and other crew members.