Conveying condolences to Russian President Vladimir Putin, Mr Mukherjee said: "Please accept my heartfelt condolences for the loss of innocent lives in the blast that occurred in the Metro system of St. Petersburg yesterday (Monday)."
Extending his sympathies to the families of the victims of the blast, Mr Mukherjee said: "This is yet another reminder that the menace of terrorism must be addressed urgently and comprehensively by the world community."
"We pray for the early recovery of all those injured in the attacks," he added.
President Putin, who was in the city when the blast occurred, visited the scene on Tuesday evening.
The suspect, Akbarzhon Jalilov, has been identified as a Kyrgyz national with Russian citizenship.