Niger's defense ministry said the insurgents attempted a quiet attack mounted on the lake's waters.
"Some 100 Boko Haram fighters arrived in four large wooden canoes and an armed speedboat" and attempted to attack troops on the islets of the lake, which borders Niger, Nigeria, Cameroon and Chad, the defense ministry said.
It added that government troops "forced the assailants to flee with several dead in their ranks."
But, defense officials said "On the army side, seven soldiers were injured when their vehicle was blown up by an improvised explosive device."
The ministry went on to say the engagement with jihadis "led to the neutralization of some 40 fighters" and the recovery of several weapons along with ammunition and explosives.
Niger, Nigeria, Cameroon and Chad revived the Multinational Joint Task Force (MJTF) in 2015 to fight the extremists.
The forces launched a new offensive in March that aimed to "completely destroy Boko Haram and other terrorist groups which plague the basin," a senior MJTF official, who wished to remain anonymous, told AFP earlier this month.
The joint force killed some 20 jihadis in an operation in early May.
Boko Haram launched an insurgency in northeast Nigeria in 2009 before it spread to neighboring countries.
More than 36,000 people have been killed since, mainly in Nigeria, and 3 million were forced to flee their homes, the United Nations says.