According to reports, the attack occurred on Sunday when Sri Lankan naval officers hurled stones and bottles at the boat which injured one Indian fisherman. The boat carried four fishermen.
Navy Spokesperson Akram Alavi has denied the reports and said such an attack did not take place.
"If such an incident had occurred, the navy would have been notified immediately. But nothing of this sort has taken place," Alavi told Xinhua news agency.
The Sri Lankan navy last week arrested 14 Indian fishermen for poaching in local waters.
Both the countries have been trying to resolve the long-standing fishermen issue with both sides having to face arrests and boats being detained when they stray into each other's waters.