Rajput, 34, was found dead in his flat in Mumbai on 14 June. Police said he had killed himself.
His family, however, registered a police complaint against Chakraborty, accusing her of abetment to suicide.
She is yet to comment but denied any wrongdoing in earlier statements.
Authorities are yet to reveal the charges against her.
Chakraborty's brother, Showik, and Rajput's former house manager, Samuel Miranda, were also arrested last week in the same drugs case.
But the charges against them have not been revealed either.
Chakraborty's is the most high-profile arrest in connection with a case that has captivated and polarised India in recent months.
Prime time television news covered every development, turning Rajput and Chakraborty's personal lives into subjects of public debate.