The 40-year-old fisherman from Karaikal in Union Territory of Puducherry, part of a group of fishermen who had put to sea from Kodiakarai in Tamil Nadu's Nagapattinam district, was injured in the shoulder, Assistant Director of Fisheries at Nagapattinam, Gunasekaran said.
The Lankan naval men had opened fire in the air and then at the fishing boats, causing extensive damage to the boats also, the official said.
The fishermen said they were fishing in Indian waters when they were fired at.
The injured fisherman has been admitted to Nagapattinam Government Hospital.
Meanwhile, Rameswaram Fishermen's Association president Emiret said such incidents recurred due to "indifference" of the central government to the fishermen's problems.
The fishermen had lost hundreds of fishing nets and boats in such attacks and several fishermen had suffered injuries and many had died, he alleged.
On February 26, a group of fishermen from Tamil Nadu were allegedly attacked by Lankan naval men while they were fishing near Katchatheevu, an islet in the Palk Straits ceded to Sri Lanka by India in 1974.
Sixteen fishermen from the state were detained by Lankan Navy on Sunday, prompting Chief Minister Jayalalithaa to write to Prime Minister Manmohan Singh seeking his intervention to secure their early release.
"I am pained to point out that the incidents of apprehension and harassment of innocent Indian fishermen by the Sri Lankan Navy have become a regular occurrence in the past few months creating a feeling of insecurity and fear among the fishermen community," she had said.
The fishermen from Tuticorin district were arrested on the charge of violating Sri Lanka's maritime boundary.
Sri Lankan Navy said 16 fishermen were arrested, but a Tamil Nadu fisheries official on Wednesday had said, 22 were detained.