The reported death toll is among the highest since President Muhammadu Buhari came to power in 2015 and comes as the country prepares for elections in three months.
The worst losses came when militants overran a military base in the village of Metele in the north-eastern state of Borno on Sunday.
The area is the centre of an insurgency waged by Boko Haram, which was founded nine years ago to bring strict Islamic law to swaths of Nigeria, and a second newer group linked to Islamic State.
Nigeria’s military and government have repeatedly said they are on the point of defeating the militants. However, raids on military bases have continued over recent months, inflicting significant casualties. One assault on an army post on the border with Niger in September left 48 people dead.
An officer among the troops attacked at Metele told Reuters: “The insurgents took us unawares. We lost about 100 soldiers. It is a huge loss.
“We all [ran away] because we didn’t know where the bullets were coming from. They killed some of us who went to evacuate the bodies of the killed soldiers. We left our armour, tanks and weapons … The village is still under their control.”
Islamic State said on Monday it was responsible for the Metele attack and claimed to have killed at least 40 Nigerian soldiers.
On Thursday, the senate, which is controlled by the opposition People’s Democratic party, suspended its session in honour of the soldiers who died at Metele, and put the death toll at 44.
A soldier who survived the assault, told the Vanguard newspaper that at least 70 soldiers were killed, blaming a lack of “adequate weapons” and ammunition.
Reuters said four security sources had put the total at about 100.
The increase in violence in north-east Nigeria follows a power struggle among militant leaders.
In the first major rift, the Isis-linked group split from the one led by Boko Haram’s veteran leader, Abubakar Shekau, after arguments over his indiscriminate targeting of civilians in raids and suicide bombings.
Analysts believe this breakaway faction, known as the Islamic State in West Africa, has a new hardline leadership after a further internal struggle and is responsible for the recent kidnapping and killing of aid workers.
A study by the Centre for Strategic and International Studies, a US-based thinktank, estimated there were between 3,500 and 6,900 Islamist fighters in Nigeria.
The study concluded there were at least three times as many armed jihadis today than before the 9/11 attacks of 2001.
The Nigerian army has been hit by a series of mutinies as soldiers refuse deployments to the frontline in the north-east, saying they lack basic equipment and supplies, including adequate weapons and ammunition.
A spokesman for the presidency on Thursday said the military would issue a statement, while the military did not respond to requests for comment. The government and military often decline to acknowledge the scale of losses in the north-east.