I would like to know about the application of cryptography in India during the last 3000 years. Most of the historical accounts of cryptography are from the Roman empire or WWII. Are there any historical records of Indian rulers communicating in cipher texts?
This is likely to be a pretty broad question as cryptography was known to the ancient Indians.
You could start with the Karmasutra, which advised its readers to discretely communicate via Mlecchita Vikalpa ("the art of understanding writing in cypher, and the writing of words in a peculiar way")
Although the composition date for the Karmasutra isn't well known (sometime between 1st and 10th Century CE), it certainly fits the "medieval" scope of your question here.
The Karmasutra text doesn't state the actual method of encryption, only that it can be used. This of course implies that the practice was well known before this time.
So this is where I'd advise you to start looking and work back from there.
Obviously, reading the rest of the Karmasutra is entirely optional, but likely won't teach you more about cryptography.