"INEC (Independent National Electoral Commission) has always said that it is preparing to conduct elections in all the 36 states and the Federal Capital Territory, including the three northeast states experiencing the challenge of insurgency," said the body's chairman, Attahiru Jega.
But he added: "There are areas that are occupied by insurgents and obviously it stands to reason that elections are unlikely to take place in these areas."
Boko Haram has seized dozens of towns and villages in Yobe, Borno and Adamawa states in the last six months as part of its quest to establish a hardline Islamic state in the region.
It now reportedly controls the border areas of Borno state with Niger, Chad and Cameroon.
The territorial gains have led to fears of a total loss of government control in the remote region, with hundreds of thousands of people made homeless within Nigeria by a relentless wave of attacks.
The country's main opposition has said that those people risked being disenfranchised, which could call into question the overall election result.
But Jega said efforts were under way to enable internally displaced persons to cast their ballots, he stated.
"We are doing everything possible to ensure that elections are conducted in these three states," Jega said.
INEC on Tuesday published a list of the 68,833,476 registered voters for the February general elections.
The two main contenders in the February 14 presidential election are incumbent Goodluck Jonathan and General Muhammadu Buhari, a former military ruler.
There are a total of 14 presidential candidates, including one woman. Parliamentary elections are being held on the same date. Two weeks later, voters choose new governors and assemblies in 29 out of Nigeria's 36 states.