He is facing a secret trial in Maiduguri, capital of Borno State over what happened to 21 anti-aircraft guns assigned this year to his artillery brigade.
The brigade commander, not yet identified, claimed before his arrest that he only received one gun, the Associated Press reported.
Maj. Gen. Lucky Irabor, the theatre commander in northeastern Nigeria, told a news conference last week that military authorities have confirmed that some soldiers were selling arms and ammunition to Boko Haram.
He called it a betrayal of the Nigerian people. He gave no more details.
The admission comes three weeks after the Nigerian army said a military tribunal is trying 16 officers and troops accused of offences related to the fight against Boko Haram, including the theft and sale of ammunition.
President Muhammadu Buhari has blamed corruption for the deaths of thousands in the seven-year Islamic uprising that has killed more than 20,000. Children who escaped Boko Haram are dying of starvation in refugee camps in the northeast, where the government is investigating the alleged theft of food aid.
In addition, a slew of retired and current military officers are being investigated for diverting hundreds of millions of dollars budgeted to help curb the Islamic uprising.
Among them is Alex Badeh, a four-star general whom Buhari fired from his post as chief of defense staff. Witnesses have told a Federal High Court that Badeh stole the equivalent of $24 million budgeted for salaries in 2013 and built a shopping mall in Abuja, the capital.
Before Buhari took power, soldiers told the AP they were forced into battle with just 30 bullets each and no food rations.
They said Boko Haram was better armed and that their officers were stealing parts of their salaries and allowances.
Many ran away when the extremists attacked, allowing Boko Haram to take control of a large swath of northeastern Nigeria in 2014.
Under Buhari, a former military leader, a multinational force has retaken most towns but Boko Haram continues to carry out occasional hit-and-run attacks reports elingonews.com.