"The TDP has been fighting the anti-people policies of the Congress for three decades now. Extending support to Congress nominee Pranab Mukherjee is not acceptable," Naidu said.
Similarly, supporting the candidature of NDA's P A Sangma, backed by the "communal" BJP, would also be inappropriate.
"After lengthy deliberations on this in the party, we have decided to stay away from voting in the Presidential election," the former Chief Minister said.
The TDP has six MPs in Lok Sabha and five in Rajya Sabha.
It has 86 MLAs in AP but two of them have been siding with Kadapa MP and YSR Congress chief Y S Jaganmohan Reddy.