A report by the commission said troops retaliating against civilians have torched homes and tried to hide evidence of gross violations by disposing of bodies.
In the most egregious case, where troops went on a rampage in several villages after a soldier was killed in mid-April in the fishing village of Baga, it quoted police as saying soldiers "started shooting indiscriminately at anybody in sight including domestic animals. This reaction resulted to loss of lives and massive destruction of properties."
The military said 36 people were killed, most of them extremist fighters. Witnesses told the AP at the time that some 187 civilians were killed.
The commission said the killings also came after militants had ransacked an armory, with subsequent reports indicating the extremists enjoyed an increase in the caliber and quantity of weapons and "had become both more organized and emboldened by their apparent successes despite the enhanced security presence."
That contradicted military reports that they have taken control of the region in a military emergency covering three states and one-sixth of the sprawling country. Instead, they appear to have pushed the fighters into rocky mountains with caves where it is more difficult to flush them out. The extremists regularly attack towns and villages.
The commission, a government body, issued an interim report saying it would finalize it when its investigators are able to visit the area where soldiers have cut mobile phone and Internet connections. A state of emergency was declared May 14 when the government said extremists from the Boko Haram terrorist group had taken control of some towns and villages.
The insurgency poses the biggest threat in years to security in Nigeria, Africa's most populous nation of 160 million and the continent's biggest oil producer.
Communities trapped between the Islamic militants and the security forces "reportedly live in desperate fear and destitution," the commission said.
It warned of an imminent public health emergency and food shortages because farmers have been forced from their fields.
Food prices have nearly trebled, the commission said, with a 50-kilogram (110-pound) sack of rice selling for up to 18,000 naira ($112.50) from 7,000 naira ($44).
Some medical experts from the region have reported a notable upsurge in sudden deaths, heart attacks and aneurysms, it said.
Northeast Nigeria already presents "the worst statistics of human development in Nigeria generally," it said.
Maternal mortality rates were three times the national average of 545 deaths for every 100,000 live births, and reports reaching the commission suggest the emergency has even more mothers dying in childbirth.
Northeast Nigeria is the poorest region in the country, with government statistics indicating 75 percent of the population lives from hand to mouth on less than $1 a day.
The commission's interim findings corroborated AP reports from the region. Militants who began by targeting government personnel and health workers — they preach that Western religion and medicine are forbidden — are increasingly targeting civilians in attacks on schools and vaccination campaigns.
"The Commission equally received several credibly attested allegations of gross violations by officials of the JTF (joint task force of police and military), including allegations of summary executions, torture, arbitrary detention amounting to internment and outrages against the dignity of civilians, as well as rape," the rights commission said.
"In particular, we have received persistent and credibly attested allegations of indiscriminate disposal of dead human remains by personnel of both the JTF and the Borno State Environmental Protection Agency."
The military and presidential spokesmen did not respond to requests for comment.
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