"Israel has lost a statesman who made courageous efforts to achieve peace for his country and the region," said Mukherjee in his condolence message to Israeli President Reuven Rivlin.
"Peres was a visionary who strongly believed in the power of knowledge, innovation and technology," said Mukherjee.
The President said Peres would be remembered as a steadfast friend of India and his lasting contribution to the strengthening of bilateral partnership between the two countries would be long remembered.
"In former President Shimon Peres, we lost a key world leader and a friend of India," tweeted Modi, expressing his grief.
Mourning the Israeli leader's death, Congress President Sonia Gandhi said Peres gave strength and goodwill to Indo-Israeli relationship.
Describing him as a defining political figure, Gandhi said Peres would be remembered as a steadfast pacifist and a believer in peace and coexistence.
Veteran Bharatiya Janata Party leader and former Deputy Prime Minister L.K. Advani called the Israeli leader a "warrior for peace".
"He was Israel's warrior for peace," said Advani and noted that Peres held several diplomatic and military positions during and after Israel's war for independence.
"I had the privilege of meeting him personally on a couple of occasions and found him to be a man of very broad vision," added Advani.
Peres, 93, a Nobel Peace laureate and one of Israel's founding fathers, died on Wednesday at a hospital in Tel Aviv. He was in the hospital for two weeks following a major stroke.
An admirer of India who supported India for a permanent seat on the UN Security Council, Peres visited India twice, in August 2000 and January 2001 as Minister for Regional Cooperation. He visited India the third time in January 2002 as Deputy Prime Minister and Minister of Foreign Affairs.
