The actress played a pregnant woman who returns to India to search for her husband during a religious festival in the Sujoy Ghosh-directed movie.
Ghosh tweeted: "Writing begins. I have no idea how Balan is going to pull this off.
"But mine is not to question how, mine is but to write right now.
Ghosh added later: "I'm told, just now, that Kahaani completes 75 days today :) good day to start writing for the Balan (sic). she will be back."
Balan has previously praised Ghosh's writing, describing it as the film's unique selling point.
She said: "It was challenging yet fun to shoot on the streets of Kolkata. I feel at home there, and I have shot two films there before."
Ghosh last week said that it was unlikely that the film will have a prequel, even though fans were keen on reviving the character of Bob Biswas.
Watch a trailer for Kahaani below: