He was critically ill and with complications resulting from non-alcoholic liver cirrhosis.
Neelabh 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.
He steered the re-launch of National Herald, the newspaper.
"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", Mr Gandhi tweeted.