The Lankan navy men allegedly pelted stones damaging the boats and the fisherman suffered head injuries, fisheries department officials said.
The fisherman was discharged after treatment at a hospital, police said.
In two separate incidents over the past nine days, 14 fishermen have been injured and 23 boats damaged when Lankan Naval personnel allegedly pelted stones at them while they were fishing near Katchatheevu.
On November 7, Chief Minister Jayalalithaa wrote to Prime Minister Manmohan Singh expressing concern over the frequent attacks on fishermen and said India should take a "strong stand" against Sri Lanka and "convey its serious apprehension through tough words and action".
She had said the attacks should be viewed as a national issue and not as an isolated problem of Tamil Nadu.
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