The military has promised to investigate the incident and punish the perpetrators of the inhuman abuse.
In the footage, officers in complete military fatigues, forced several young men, stripped to their boxer shorts, to lie before them, face down in muddy water.
The video is undated but it's been suggested to be recent - a fallout of the bloody clash between members of the IPOB and law enforcement in recent times.
The location of the video appears to be somewhere in Abia state where separatist Biafra agitations have since turned violent.
In reaction to the video, the military has promised to investigate the incident and punish the perpetrators of the inhuman abuse.
This was disclosed in a press statement signed by the Deputy Director, Army Public Relations 82 Division Nigerian Army, Colonel Sagir Musa, on Thursday, September 14, 2017.
The statement read, "The attention of the Headquarters 82 Division Nigerian Army has been drawn to a video clip trending on social media and other platforms purportedly showing troops humiliating some people at a check point in Abia State, Nigeria.
"The issue is being investigated with the view to ascertain the source and the actors in the clip. Our Code of Conduct and Rules of Engagement are quite clear and any officer or soldier that infringed on any of such directive if found guilty, will face full wrath of the military justice system.
"We do not condone any act of indiscipline in the conduct of our operations and training exercises. Any claim of rights violation would be investigated and when confirmed, appropriate disciplinary action would be taken against the erring personnel. "
He further accused IPOB of deliberately misinforming the public and spreading propaganda to fuel their separatist cause.
He said, "We would like inform the public that 82 Division is also aware of the planned misinformation and propaganda arrangement by the secessionists Indigenous People of Biafra (IPOB).
"They intend to churn out prerecorded video clips aimed at discrediting the Nigerian Army, causing disaffection among the citizens of this country. They will be using bogus, manipulated and photo-shopped photographs as well as video clips.
"The public should be wary of such mischief, scrutinize and report same to the Nigerian Army or any of security agencies."
This is coming off the back of a week of unrest in the state with soldiers of the Nigerian Army clashing with members of IPOB and their leader, Nnamdi Kanu.
A detachment of the Nigerian Army had been present around the home of the IPOB leader on Tuesday, September 12, creating heightened tension with members of the group only days after soldiers clashed with them while trying to gain access to the group's leader's house on Sunday, September 10.
While reports indicated that soldiers had tried to gain access into Kanu's father's compound in Umuahia and shot at IPOB members who formed a human shield to keep them out, the army dismissed the claims and said the soldiers had been attacked with stones while passing through the residence in a new armoured carrier.
While reacting to the incident on Monday, September 11, Kanu accused Chief of Army Staff, Lieutenant-General Tukur Buratai, of trying to incite his group into arming themselves to deliberately provoke a war.
He said, "Nigeria is bringing war to us, we're not fighting anybody. It is Buratai and his men that are bringing war unto us.
"They want us to become armed so that the world can say that Nnamdi Kanu is leading a violent armed group, which is not the case. They're provoking us to war."
The clashes between the opposing sides led to state governor, Okezie Ikpeazu, declaring a dusk to dawn curfew that has been extended till Friday, September 15.