Mozambique's Defence Minister Jaime Neto has said that a video showing people dressed in army uniforms beating and killing a naked woman was doctored.
The culprits had been identified and would be punished, he added.
The video caused outrage after it was circulated on social media. The defence ministry promised to investigate.
The video was said to have been filmed in the gas-rich Cabo Delgado province, where government troops are battling militant Islamists.
The militants are known as al-Shabab, and have pledged allegiance to the Islamic State militant group.
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.
Government forces have been accused of human rights abuses while trying to put down the insurgency.
Several rights groups shared the two-minute-long clip of the alleged killing of the woman on Monday.
In the video, a group of men wearing army uniform surround a woman, one hits her in the head and body with a stick several times before others shoot.
The defence ministry condemned the footage as "horrifying" and said it would carry out an investigation to establish whether it was authentic.
Speaking on a local television station on Wednesday, Mr Neto said the video had been edited by "malicious people" to denigrate the image of the military.
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 with operations to restore peace in the region, Mr Neto added.
Last week, Amnesty International said it had analysed and verified videos showing attempted beheadings, torture and other ill treatment of prisoners, the dismemberment of alleged fighters and possible extrajudicial executions.
But the government denied the allegations, saying the insurgents were known to "impersonate soldiers".
Cabo Delgado is home to one of Africa's biggest liquefied natural gas projects.
Exxon Mobil is a major investor in the development of natural gas projects worth $60bn (£45bn) off the region's coast.