In a tweet from its official account, the army said that “mopping up” operations were continuing.
It also claimed in a separate statement that it had killed many Boko Haram militants, though this has not been independently verified.
Nigeria says 150 people died when Boko Haram took Baga and nearby Doron Baga, but locals said up to 2,000 died.
Residents were left largely undefended as the military deserted when the jihadists attacked the towns.
This time, the army claims it was the militants who fled, with some drowning in Lake Chad as they tried to escape the aerial bombardment.
It added that 1,000 mines had been laid in Baga, which soldiers had to negotiate before entering.
The massacre there is regarded as the worst attack of Boko Haram’s six-year insurgency. Thousands fled across Lake Chad when the assault began with 7,000 taking refuge in the Chadian town of Ngouboua.
Also on Saturday, Niger’s army reported the deaths of 14 Boko Haram militants following clashes in an island on the Niger side of Lake Chad.
“Seven Niger soldiers were killed and two others wounded in a Boko Haram attack on a village near Lake Chad on Friday night,” a military report said. “Boko Haram lost 14 members.”
The fighting took place in Karouga, near the border dividing Niger, Nigeria and Chad, a Chadian security source said.
According to the source, Boko Haram members later sought to enter Chadian territory by crossing Lake Chad, but Chadian aircraft intervened and destroyed their five boats.
Boko Haram has in recent weeks extended its violent campaign across Nigeria’s north-eastern border into neighbouring countries as regional forces pursue the Islamists.