He was critically ill and with complications resulting from non-alcoholic liver cirrhosis.
Mishra, 57, was admitted to Apollo Hospital in Chennai earlier this month, and developed multiple organ failure before a liver transplant could be carried out.
Mishra steered the re-launch of National Herald, the newspaper.
Congress chief Rahul Gandhi condoled his death, describing him as one who spoke the truth to power.
An editor's editor. A man who spoke truth to power. An institution builder. On Neelabh Mishra's tragic passing away this morning, my deepest condolences to his family, friends, colleagues and admirers, he tweeted.