"There is no personal thing involved here... Commissioners have no choice but to apply the constitution... Once you have been indicted, INEC cannot do anything about it," Maurice Iwu, the INEC chairman, said in a press conference.
Abubakar says the indictment is unconstitutional and politically motivated, and has challenged it in the courts.
Iwu said any legal challenge to the list would be appealed by the commission.
Diplomats say the omission of Abubakar, who would have been one of three front-running candidates in a close race, will hurt the credibility of the poll, which should mark the first transition from one elected government to another in Nigeria's 47-year independent history.
The list of approved candidates included the names of Umaru Yar'Adua, the presidential candidate of Olusegun Obasanjo, the ruling People's Democratic Party (PDP) president, Muhammadu Buhari of the All Nigeria Peoples Party (ANPP), and Emeka Odumegwu-Ojukwu of the All Progressives Grand Alliance (APGA).