In his message to Rivlin, the President said that "on behalf of the government and the people of India, I extend my heartiest felicitations to you on your victory in elections to the high office of the President of the State of Israel."
He said the relationship between the two countries had deepened in diverse areas of mutual interest.
"We attach priority to our relations with Israel and seek further strengthening of our mutually beneficial cooperation in areas such as trade and economy, security, culture and people-to-people exchanges," the President said.
Mukherjee said India and Israel are two of the leading knowledge economies of the world and "we look forward to working towards building a strong hi-tech partnership based on science, research and innovation."
74-year-old Rivlin, a former Speaker of Knesset, national legislature of Israel, was elected 10th President on June 10 and would be sworn-in on July 24 replacing Shimon Peres.