Nigerian government and military officials have refused to comment, and it's impossible to know how many of the dead had Boko Haram connections. But Nigerian law stipulates that even under a state of emergency, detainees are supposed to be brought before a magistrate within 48 hours and to have access to lawyers and family members.
A pastor said he was held at Maiduguri's Giwa Military Barracks after he and four other people were arrested because weapons were found hidden in the shoe factory where he works.
He described hundreds of naked people crammed into a cell meant for a couple of dozen. Once a day, he said, a soldier would throw a loaf of moistened bread into the cell to be brawled over. Some died of torture, he said.
He told the AP he was freed with the intervention of a Christian group, and his jailers' recognizing his prayers for salvation as Christian. He requested anonymity fearing military retaliation.
Amnesty International reported this week that hundreds are dying in detention: some taken from the cells and shot, some dying of suffocation or starvation.
The London-based human rights group said "credible information" from a senior Nigerian army officer indicated more than 950 people have been killed in the first six months of this year. The mortuary records seen by the AP list 3,335 bodies in that period, in just one hospital.
That figure alone is about nine times greater than the 400 civilians killed in Boko Haram attacks in the same period, according to an AP count of reported incidents.
However, Boko Haram has also done much to alienate public opinion. Fighters suspected of belonging to it have gunned down dozens of schoolchildren, some as they sat at their desks writing exams,and burned alive boarding school students locked into dormitories that were set ablaze.
The name Boko Haram roughly means "Western education is forbidden."
The group has also killed many more Muslims than Christians. In August, it gunned down 47 worshippers in a mosque. Last month it captured a muezzin, made him issue the pre-dawn summons to prayer and then killed at least seven elderly men who answered the call.
Local and international human rights groups say the troops deployed to combat Boko Haram are notorious for their excesses and have draconian powers to raid homes and detain people. They see a danger of a backlash from a poor population that feels marginalized and remote from the political center of Nigeria and its Christian president, Goodluck Jonathan.
The religions co-exist peacefully in the rest of Nigeria although fundamentalism, fueled by poverty and marginalization, has been growing among Christians and Muslims in the north.
Just days after the emergency was declared, U.S. Secretary of State John Kerry noted "deep concern over credible allegations of gross human rights violations by Nigerian security forces." And in September, when he met Jonathan at the U.N., President Barack Obama "underscored the importance of countering terrorism via a comprehensive approach that creates economic opportunity and protects human rights," according to a State Department official.
On Thursday Nigeria was elected to a two-year seat on the U.N. Security Council. According to presidential spokesman Reuben Abati, President Jonathan believes it is "a glowing expression of support and encouragement for Nigeria's active participation in the promotion of peace, security and political stability in Africa and other parts of the world."
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Associated Press writer Deb Riechmann contributed to this report from Washington, D.C.