In a message to his wife, Jamila Verghese, Mukherjee said: "I am saddened to know about the passing away of your husband. Verghese was one of India's most eminent journalists and a relentless champion of freedom of the press."
"In his death, the nation has lost an outstanding scholar, influential opinion maker and a crusader for civil rights. His life and writings will continue to be a source of inspiration and guiding light for journalists as well as the people of our country."
"Please convey my heartfelt condolences to all members of the bereaved family and his countless friends. I pray to the Almighty to give you and your family the strength and courage to bear this irreparable loss," he added.
Vice President Hamid Ansari said that the country has lost "a fearless commentator and a prolific writer".
"I am profoundly saddened at the passing away of Verghese, a doyen of Indian journalism, and amongst the most versatile and influential intellectuals of our country," he said.
"In a long and illustrious career in journalism, Verghese wrote on diverse issues ranging from civil liberties and human rights, especially of the weaker and marginalised sections of society, to rural development, environment and national security, with a focus on non-traditional security issues."
"In his departure, we have lost a fearless commentator and a prolific writer who made valuable contributions to the national debate on important issues of public interest and concern," he added.
Verghese, an acclaimed editor, was also a highly respected columnist. The 87-year-old breathed his last Tuesday at his son's residence in Gurgaon. He is survived by wife and their two sons.