Mozambique’s Defense Minister Jaime Neto has said a video was shown showing people dressed in army uniforms beating and killing a naked woman.
The culprits had been identified and would be punished, he added.
The video created outrage after it was circulated on social media. The Ministry of Defense promised to investigate.
The video is said to have been filmed in the gas-rich province of Cabo Delgado, where government troops are fighting militant Islamists.
The militants are known as al-Shabab and have pledged allegiance to the militant group of the Islamic State.
They have carried out a series of attacks on villages and towns in the area over the past three years, leaving more than 1,500 people dead and at least 250,000 homeless.
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Government forces have been accused of human rights abuses while trying to quell the uprising.
Several rights groups shared the two-minute-long clip of the alleged murder of the woman on Monday.
In the video, a group of men wearing army uniforms surround a woman, one hits her in the head and body with a stick several times before others shoot.
The Department of Defense condemned the footage as “horrific” and said it would conduct an investigation to determine if it was authentic.
Speaking at a local TV station on Wednesday, Mr Neto said the video was edited by “malicious people” to tarnish the military’s image.
He did not give further details, but said the people responsible for creating the video would be paraded in front of the public and punished.
Troops would continue operations to restore peace in the region, Mr Neto added.
Last week, Amnesty International said it had analyzed and verified videos showing attempts at beheading, torture and other ill-treatment of prisoners, the division of alleged fighters and possible extrajudicial executions.
But the government denied the allegations, saying the rebels were known to “imitate soldiers”.
Cabo Delgado is home to one of Africa’s largest liquefied natural gas projects.
Exxon Mobil is a major investor in the development of natural gas projects worth $ 60 billion. (£ 45bn) Off the coast of the region.