Banerjee, who is seen as a potential prime ministerial candidate, said that she stood behind the Indian Armed Forces, but that they should be given a chance to speak the truth.
"We don't want a war for political reasons, to win an election," she said.
Modi has accused the opposition Congress party, and other opponents such as Banerjee, of helping India's enemies by demanding evidence of the attacks.
"At a time when our army is engaged in crushing terrorism, inside the country and outside, there are some people within the country who are trying to break their morale, which is cheering our enemy," Modi said at an election rally on Sunday.