Police said the charge sheet was filed after prima facie evidence was found against Chowdhury by the probe team.
Angry over the development, the Youth Congress has decided to take out rallies in Baharampur.
The State Congress in a statement said Chowdhury was being framed on trumped-up charges and declared it would launch protests outside every police station.
"This is a conspiracy against Chowdhury. We had a hunch the government could take such an unjust step. This is wrong. This is politically motivated," said state Congress chief Pradip Bhattacharya.