Al Nahyan, who is on a three-day visit, was accorded a ceremonial Guard of Honour in the sprawling courtyard of the Rashtrapati Bhavan in what is his first state visit to India.
Prime Minister Narendra Modi, Home Minister Rajnath Singh and Finance Minister Arun Jaitley were present on the occasion.
Modi and Al Nahyan, who is also the Deputy Supreme Commander of the UAE armed forces, later met at the Prime Minister's residence.
"An exceptional tete-a-tete. PM meets the Crown Prince for a restricted meeting at 7RCR before talks in the evening," Ministry of External Affairs spokesperson Vikas Swarup tweeted.
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Ways to contain radicalism, stepping up counter-terrorism cooperation and dealing with the ISIS are likely to figure prominently in the talks.
Before his ceremonial welcome, the Crown Prince also visited Mahatma Gandhi's memorial at Rajghat, laid a wreath and planted a sapling there.
Al Nahyan arrived here yesterday to a warm welcome, with the Prime Minister keeping aside protocol to receive the "special friend" at the airport with the hope of adding new vigour and momentum to India-UAE ties.