Sen, the group's chairman, along with Mukherjee and Arvind Singh Chouhan, who looked after the company's interests in Jharkhand, were produced before Additional Chief Judicial Magistrate A H M Rahman court in Bidhannagar.
The three were charged under IPC sections 406 (criminal breach of trust), 420 (cheating) and 506 (criminal intimidation).
The court said that Sen could have a lawyer during interrogation if he desired and also asked the Bidhannagar police commisionerate to provide details of pending cases in their jurisdiction against the trio within a week.
Meanwhile, Deputy Commissioner of Bidhannagar police Arnab Ghosh said that Mukherjee was a key decision-maker.
"We have come to know that Debjani had played a role in the decision-making process of Saradha," he said.
Asked why the other Saradha directors were not arrested, Ghosh said all directors were not part of the decision-making process and cited the example of Hemant Pradhan who was actually a cook and had no idea that he had been made a director.
Outside the court, placard-waving Youth Congress and BJP workers held demonstrations demanding that Sen be punished for duping thousands of investors and action against TMC MPs whose names figured in the scam.