Mr Mukherjee also conveyed to Russian President Vladimir Putin that people of India stand by Russia in this difficult hour.
In a message to Vladimir Putin, the President conveyed his condolences on the loss of lives in the blast in a metro carriage in St Petersburg yesterday.
"This is yet another reminder that the menace of terrorism must be addressed urgently and comprehensively by the world community," he said.
Mr Mukherjee said the people of India stand with the Russian people in this difficult hour and offer their sincere sympathies to the families of the victims.
"Please accept my heartfelt condolences for the loss of innocent lives in the blast that occurred in the metro system of St Petersburg.
"We pray for the early recovery of all those injured in the attacks," he said.
A suicide bomber was behind the attack that killed 14 people and left dozens wounded.