The meeting was described as a courtesy call by the Andhra Pradesh government, but it assumed significance against the backdrop of the war of words between Telangana and Andhra Pradesh over the cash-for-vote controversy and allegations of phone tapping.
Naidu had met Prime Minister Narendra Modi earlier this month and demanded a probe into alleged phone tapping by Telangana government.
Meanwhile, common Governor of Andhra Pradesh and Telangana ESL Narasimhan also met the President today.
The President arrived here yesterday for the customary southern sojourn during which he stays at Rashtrapati Nilayam, one of the Presidential Retreats.
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On July 3, the President will receive the first copy of book 'Uniki' written by Maharashtra Governor C Vidyasagar Rao at the Hyderabad International Convention Centre, it said.
Mukherjee would also inaugurate 'Nakshatra Vatika' (constellation garden) at Rashtrapati Nilayam on July 6. His stay here will end on July 8.
The Rashtrapati Nilayam building earlier belonged to the Nizam of Hyderabad. Constructed in 1860, the building premises are spread over 90 acres.