The Joint Task Force (JTF) was stationed in the north to fight against the upsurge of Islamic extremists in the region spearheaded by Boko Haram sect.
During the attack on the town, the Red Cross reported that 187 persons were killed but the military said the number was much lower.
HRW said images released suggest that 2,275 buildings were destroyed with 125 severely damaged whereas the country's President Goodluck Jonathan had said after receiving a report from the military yesterday that the destroyed buildings were not up to 1,000.
Maina Ma'aji Lawan, a senator representing Baga in the Parliament, alleged that 4,000 houses were destroyed while 200 people were killed.
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Nonetheless, some observers noted that northern communities shielded terrorists in their houses.
Jonathan has promised that the country's Human Rights Commission (HRC) would investigate the incident despite an initial probe carried out by the military and National Emergency Management Agency (NEMA).
Boko Haram carries out frequent attacks on police stations and other public institutions in the northern part of the oil rich African country.
Since it commenced attacks in 2009, more than 4,000 lives have been lost.