Defense Ministry spokesman Brig. Gen. Chris Olukolade said Tuesday some will be redeployed immediately.
A battalion is about 700 soldiers. Nigeria had sent 1,200 troops to aid an African force helping put down an Islamic insurgency in northern Mali.
Olukolade said Nigeria will sustain its contribution to the operations in Mali "in other forms," including providing a fully staffed military field hospital, a signal squadron and staff officers for the force headquarters.
The African Union said earlier this month that Nigeria would withdraw some troops to fight an Islamic uprising in its northeast.
Some soldiers fighting in northeast Nigeria have complained to The Associated Press that they have been deployed for more than two years, thousands of miles from their families.
Human rights activists say the lack of rotations could be contributing to ongoing reports of human rights abuses by soldiers—charges the military denies.