The meeting took place at New York's Palace Hotel on the sidelines of the UN General Assembly during which Modi and Netanyahu discussed a wide range of issues including defence cooperation and the situation created by the Islamic State (IS) in West Asia. Both the leaders are staying at the Palace Hotel.
During the 30-minute meeting, Netanyahu invited Modi to visit Israel at an early date.
The Spokesperson said Prime Minister Modi has taken note of the invitation and this would be discussed further through diplomatic channels.
He said the two leaders discussed ways to enhance economic cooperation and Israel offered expertise in water management and other agricultural-related areas.
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India and Israel have a very robust relationship and currently bilateral trade stands at approximately USD six billion.
Asked if there was a discussion on defence deals, he said, "Yes there was a discussion in terms of defence ties and the Prime Minister explained that his new vision of 'Make in India' was a priority.
"He also explained that right now in defence sector Israel or any other country can invest up to 49 per cent. And the Prime Minister made a pitch for skill sharing in areas like IT and water management."
According to Netanyahu's office, the two leaders discussed Iran, the threat of terrorism, and possible cooperation in the fields of high-tech, cyber-security, water conservation and agriculture.
"We are two old people, some of the oldest civilizations on earth," Netanyahu said. "But also two democracies, proud of our tradition, but also eager to seize the future. I believe that if we work together it will be for the benefit of both our peoples."
During the meeting, Modi, who had met a Jewish group earlier, also mentioned that there was no discrimination against the community in India.
In 2003, Ariel Sharon paid the first visit by an Israeli Prime Minister to India when Atal Bihari Vajpayee was the Prime Minister.