Party spokesman Randeep Surjewala responded to BJP's allegation by saying that branding as "Pakistani" those raising questions over the matter goes against the basic tenets of democracy.
"We would request our friends in BJP to stop branding every Indian citizen asking questions as a Pakistani, for that goes against the very tenets of democracy," he told reporters here.
"As a primary opposition party, it is our responsibility that whenever in public life divisions crop up in different agencies of the government, we are in a position to put forward questions on behalf of the people to the government," he said.
His remarks came in response to charge by BJP National Secretary Shrikant Sharma that Congress was playing "dirty politics" over the boat issue.
In a mid-sea operation, a suspected Pakistani boat was intercepted by the Coast Guard in the Arabian Sea in the intervening night of December 21 and January one after which it caught fire and exploded with all four crew members on board.
While the government maintains that its occupants were "suspected terrorists" carrying explosives, there have been reports that they may have been smugglers.