Sitharaman said she spoke to Coast Guard (CG) authorities and those in Tamil Nadu soon after the alleged firing incident.
She sought details from the Coast Guard chief after seeing the reports on TV channels, the minister said on the sidelines of a CII event.
In reply to a question, she told reporters that the CG chief said that "we don't have such bullets".
"If a wrong has happened, those who did it will be definitely punished," she said, asserting that making accusations without a proper inquiry was unacceptable.
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"I understand the travails of our fishermen" and it needs to be found out who fired at them, Sitharaman said.
The ICG had on Tuesday denied that its personnel opened fire and said "no fisherman has been fired upon by any CG ship in Palk Bay".
In a statement the ICG had said it might have been an attempt by the fishermen to "divert" attention as they were checked and warned by the Indian Coast Guard Ship against "unauthorised" paired trawling.
Fishermen Care, a Chennai based association, had made a plea to the court on the incident. The Mandapam Police in Ramanathapuram district was looking into the matter.