In a strongly worded letter, Parrikar said that while political parties and politicians may have the luxury of making "wild and unsubstantiated allegations against each other", one needs to be extremely careful while referring to the armed forces.
"Your allegations in this regard run the risk of adversely impacting the morale of the country's armed forces and the same were not expected from a person of your standing and experience in public life," the Minister said.
Banerjee, who has been opposing the Centre's demonetization move, had accused it of deploying the army at toll plazas in West Bengal without informing the state government and described it as "unprecedented" and "a very serious situation worse than Emergency".
The Trinamool Congress had refused to leave her office in Kolkata till the Armymen were withdrawn from toll plazas, and had asked whether it was an "army coup", drawing sharp reaction from the Centre.
Terming it as "avoidable controversy" over the exercise carried out by the Eastern Command in West Bengal and other states under the jurisdiction to collect information about the movement of heavy vehicles at toll gates, Parrikar, in his letter to Banerjee dated December 8, said it is carried out by all formations of the army all across the country for many years.
He said the exercises are held as per the dates convenient to the army in consultation with agencies of the state government.
"I have been deeply pained by your allegations as reported in the media. If only you had enquired with the agencies concerned of the state government, you would have come to know of the extensive correspondence between the Army and the state agencies including the joint inspection of sites carried out by them," Parrikar said in his letter to Banerjee.
Describing Indian army as the "most disciplined institution of the country", he said the nation is proud of their "professionalism and apolitical conduct".
He added that the army authorities were forced to put the record straight in the matter by presenting evidence of their communication with the state agencies concerned including rescheduling of the data collection operations on their response.