In a message to Israel's President Reuven Rivlin, Mukherjee conveyed his heartfelt condolences and said he was deeply saddened to learn about the demise of Peres.
"In his passing, Israel has lost a statesman who made courageous efforts to achieve peace for his country and the region. The worldwide admiration and accolades that he received for his work - including the Noble Peace Prize, are a testimony to the values that he stood for.
Mukherjee said India remembers Peres as a steadfast friend of the country, whose lasting contribution to strengthening of the close bilateral partnership between India and Israel will be long remembered.
"I would request you, Excellency, to kindly convey my deepest sympathies to his bereaved family. May the Almighty give them the strength to bear this loss," he said.
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The President also warmly recalled his last meeting with Peres in October, 2015, during a visit to Israel.
Prime Minister Narendra Modi in a tweet said, "In former President Shimon Peres, we lost a key world leader and a friend of India. Pained by his demise. Our condolences to people of Israel."
"Peres will be remembered as a steadfast pacifist and hopeful believer in peace and coexistence," she said in a statement.
Underlining that his tenure added strength and goodwill to the Indo-Israeli relationship, Gandhi hoped that his family, friends and admirers find peace and strength in this hour of grief.
Chairman of the Committee on Ethics of Lok Sabha, L K Advani said he was deeply grieved to learn about the demise of Peres, who represented many political parties in the Knesset.
"He was Israel's warrior for peace. At a very young age, Mr Shimon Peres was elected to the Working and Studying youth national secretariat.
"I offer my heartfelt condolences to the family of Shimon Peres. May the departed soul rest in peace," he said.