Residents of this small region in the violence-torn city have accused soldiers of killing the man and his wife at their home for no reason, according the Associated Press report.
The security raid comes a few short days after the coordinated bomb and gun attacks that ripped through northern Nigeria's largest city and claimed over 160 lives.
The Boko Haram suspect was identified as Uzairu Abba Abdullahi, but was called Alhaji by residents, the Daily Trust reported. According to their report, security operatives had set upon the Abba residence in Hotor and engaged in a heated gun battle for hours.
Neither Abba nor his pregnant wife survied the onslaught. Associated Press photos of the alleged Boko Haram member's home, the site of the attack, showed bullet holes on the walls and pools of blood on the floors.
According to the Daily Trust, both corpses were whisked away immediately after the attacks by the security operatives. The AP reported that the local police commissioner, who confirmed the attacks, had said it was part of the government's efforts to crack down on terrorism and root out members of the sect.
The attack was a jarring shock for the residents who have already suffered through the horror of recent attacks on the city on Friday. The sound of gun shots kept them awak till daybreak.
"We had a sleepless night due to the operation executed in the are. In fact, we though it was the whole area that was being raided only find that it was just one house. It was really frightening and terrifying," a resident of the area told the Daily Trust.
Tuesday's killings is the latest in a string of killings carried out by security agents, following the deadly Kano city attacks. Four men had been reportedly gunned down in their car in Maiduguri by security operatives who claimed they were members of the sect.
Police and security officers have also arrested over 150 individuals, all of whom they claim have dealings with the sect. Whether or not the mass arrests are backed with proof or evidence, however, is unclear.
According to the Daily Trust, Ali Abdullahi, brother of the deceased, denied claims that Abba had been a part of the dreaded sect.
"My brother was innocent and not a member of the Boko Haram as it is believed. I know he is a practising Muslim and had beard as a Sunnah of the Prophet Muhammad and notheing more.
"What happened to him is simply indicating that no one is safe because wearing a beard is not enough prove that one is member of Boko Haram. This is really unfortunate," Ali Abdullahi is quoted by the Trust as saying.
Another relative, Musa Ibrahim Fatega, who was quoted by the AP echoed Ali's sentiment. "That means you cannot dress the way you are. Is it good? Is this how government is going to treat us?"
Security in the city has intensified following the attacks, and the police recently confirmed that 10 car bombs and about 300 unexploded devices - comprising of aluminum soda cans packed with explosive material - were also discovered by police.
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