Sen. Ahmed Zanna said Sunday he is being framed because he recently charged the Joint Task Force was killing civilians in its search for members of the Islamic extremist group, Nigerian newspaper Leadership reported.
The commander, Shu'aibu Bama, was arrested Thursday.
Zanna said he was out of town Thursday when four armored vehicles and about 40 soldiers from the JTF came to his home. They searched the home and beat up members of his household before asking them if they knew where Bama lived.
One person took the soldiers to a home near the senator's house where Bama was arrested.
The JTF had charged Bama was arrested at Zanna's home.
Zanna said the JTF made the false claim because he had recently said in a BBC interview the unit should withdraw from Borno state. He charged the JTF had burnt at least 300 homes in the last six weeks and had killed as many as 500 people.
The senator said Bama was his nephew, a drug addict who "beats up my children, he abuses my friends," and had threatened to kill his own mother.
Separately, governors from several northern states and a former president Sunday called on all terrorist groups to end their mass killings.
In a statement, the Northern States Governors Forum noted 116 people had been killed in attacks in five states this month, including the deaths of 34 people in Yobe state on Friday.
The federal government must negotiate for peace with all militant groups in the country, former interim president Ernest Shonekan said Sunday.
Speaking at a graduating ceremony at the Institute for Security Studies in Abuja, Shonekan said the federal government must immediately find "ways and means of engaging them in robust dialogue to make them see reason and eschew violence."