"The nation has lost a personality who was always in touch with the grassroots of society," Mukherjee said in a message to Deshmukh's wife Vaishali.
Describing Deshmukh as a veteran politician and an able administrator, the president said he was always concerned about the welfare of the poor and downtrodden.
"He was a towering leader of Maharashtra and his immense contribution to the welfare of the state will always be remembered," he said.
Deshmukh died in a Chennai hospital Tuesday. He was 67.