The attack, one of the deadliest recently, came as the military tried to launch an offensive against the armed group.
“We lost 92 of our soldiers, non-commissioned officers and officers,” the president said of the attack overnight on Sunday in Boma.
“It’s the first time we have lost so many men,” he added, after visiting the site of the incident in Lac province, which borders Niger and Nigeria.
The attack on soldiers on the Boma peninsula lasted at least seven hours and reinforcements sent to help out were also hit, one soldier told AFP news agency.
He said 24 army vehicles were destroyed, including armoured vehicles and Boko Haram carried off weapons stolen from the military in speedboats.
“The enemy has hit at our defences hard in this zone,” a senior officer said.
The attack is part of an expanding armed campaign in the vast, marshy Lake Chad area, where the borders of Cameroon, Chad, Niger and Nigeria converge.
Boko Haram launched an armed campaign in Nigeria in 2009 before beginning incursions in its eastern neighbours.
Earlier on Tuesday, Nigeria’s military reported that scores of Nigerian soldiers were also killed in the northeastern state of Borno near the border with Chad.
The attackers used rocket-propelled grenades and other heavy weaponry in the attack on the village of Gorgi on Monday evening.
It was not immediately clear who the attackers were, but fighters from Boko Haram and the ISIL (ISIS) West Africa Province groups are active in the region.
Boko Haram has stepped up its attacks in recent months on the islands of the Lake Chad Basin.
Since 2015, countries in the area have cooperated in the Multinational Joint Force, a regional coalition engaged around Lake Chad with the help of local residents formed into vigilante groups.
Boko Haram’s decade-long armed campaign has so far killed 36,000 people and displaced nearly two million in northeastern Nigeria, according to the United Nations.