The Defence Headquarters said Nigerian troops that were found in Cameroun was as a result of a sustained battle between the troops and the terrorists around the borders with Cameroun which saw the Nigerian troops charging through the borders in a tactical maneuver.
Cameroonian Army spokesman, Lieutenant Colonel Didier Badjek, had told BBC on Monday that the soldiers were disarmed and were now being accommodated in schools.
Nigerian defence however explained that the soldiers eventually found themselves on Camerounian soil following a fierce battle with insurgent.
“Being allies the normal protocol of managing such incident demanded that the troops submit their weapons in order to assure the friendly country that they were not on a hostile mission,” Defence spokesman, Major General, Chris Olukolade said in a statement.
He said, “Following necessary discussions between Nigerian and Camerounian military authorities, the issues have been sorted out. Subsequently, the troops are on their way back to join their unit in Nigeria.
“The reference to the incidence as a defection is therefore not appropriate considering the discussion between the two countries’ military leadership and the series of contacts with the soldiers who have confirmed that they are safe.
Meanwhile, troops are repelling a group of terrorists who are trying to enter the country through Gamborou Ngala. A group of them who fizzled into the town are being pursued.
Clashes are said to be continuing in the border town of Gamboru Ngala in Borno State, BBC reports.
Boko Haram on Sunday released a video in which it said it had established an Islamic state in the towns and villages it controls in north-eastern Nigeria.
The group’s five-year insurgency has intensified in recent months despite the deployment of thousands of extra troops to the worst-affected areas.
Last week, a group of soldiers refused to follow orders to go and fight Boko Haram, saying the militants were better equipped.
Insurgents also seized one of Nigeria’s two main police training academies, which is near the town of Gwoza, captured earlier this month.
The Nigerian soldiers are currently in the Cameroonian town of Maroua, about 80km (50 miles) from the Nigerian border, Badjek told the BBC.
Thousands of civilians are also said to have fled across the border.
In May, some 300 people were killed in an attack on Gamboru Ngala, which left much of the town in ruins.
It is near Gwoza, the largest town under control of Boko Haram.
In the most recent census, in 2006, it had a population of more than 265,000 people.
In the 52-minute video released on Sunday, Boko Haram leader, Abubakar Shekau, said Gwoza was now “part of the Islamic state”.
He did not specify whether his groups now had any links to the Islamic State group, which has seized much of northern Iraq in recent months, prompting the US to respond with air strikes.
There is no evidence for such links but in July, Shekau congratulated IS on its territorial gains.
The Nigerian military has however faulted the claim by Boko Haram that Gwoza was now under its control.
It said no part of the Nigerian territory had been ceded to anyone or group and that the military was flushing out the remnants of the Boko Haram troop in Gwoza and adjoining villages.