The results had President Muhammadu Buhari winning overwhelmingly and been retained for a second term.
Confirming the news to the BBC, the PDP spokesman Kola Ologbondiyan said the results were unacceptable.
He said the party was questioning the high numbers of votes for Mr Buhari in insurgency-hit states such as Borno and Yobe whereas the number of votes for PDP candidate Atiku Abubakar in states in the south were “reduced”.
Reuters news agency quoted another PDP official, Osita Chidoka, as saying the party would consider mounting a legal challenge against the result.
"We will explore all options including the belief that the legal process in Nigeria is one of the ways to resolve issues," Mr Chidoka said.