In a message to Bal Thackeray's son Uddhav, Mukherjee said the nation has lost a veteran leader who worked to help the common man.
"I am extremely sad to learn about the passing away of your father, Shri Balasaheb Thackeray. Shri Thackeray's passing away is a loss for the people of Maharashtra and India," the president said.
"In his death, the nation has lost a veteran leader who worked to help the common man and whose contributions in the field of media added a different perspective to the political discourse," Mukherjee said.
"Please accept my heartfelt condolences and convey the same to other members of your family and numerous followers of Shri Balasaheb Thackeray. I pray to the almighty to give you and your family the strength and courage to bear this irreparable loss," the president added.
The Shiv Sena had supported Mukherjee during the presidential election earlier this year going against the stance of its ally Bharatiya Janata Party.