Describing Shukla as "a veteran Parliamentarian, able administrator and an outstanding statesman", Mukherjee said he had made "valuable contribution to the growth of our nation in various capacities. The nation will remember his contributions and his pursuit of excellence in public life".
Mukherjee said he has lost a friend with whom he had "a long personal association".
In a condolence message to Shukla's wife, the Prime Minister said he was "particularly pained that he lost his life in a brutal attack by Left Wing Extremists. His passing away only strengthens our resolve to fight the menace of Left Wing Extremism with firmness".
He said the Congress party had lost a committed member and the country a staunch nationalist, who was "one of the most influential leaders that undivided Madhya Pradesh produced in post independence India".
Gandhi also expressed deep grief at the passing away of Shukla.
Several senior leaders, including the Prime Minister, Sonia and Rahul Gandhi, visited the All India Institute of Medical Sciences to pay their last respects to Shukla, whose body was brought from Medanta hospital in Gurgaon for embalming.
Among others who visited the hospital were senior leaders Digvijay Singh and Ghulam Nabi Azad.
Home Minister Sushilkumar Shinde also condoled the death of Shukla, while Petroleum Minister M Veerappa Moily said the ideals pursued by Shukla "will inspire the generations to come".
West Bengal Chief Minister Mamata Banerjee expressed anguish at his death, describing Shukla as a veteran parliamentarian and a senior politician.