The jihadist raid on the base was repelled and the fleeing fighters were then met by a convoy of special forces bringing supplies from the regional capital Maiduguri.
Fierce clashes between a regional force and IS-affiliated fighters in the North-east left 25 soldiers and at least 40 jihadists dead, two military sources and a militia leader have claimed.
Fighters from the Islamic State West Africa Province (ISWAP) group launched a dawn attack on Monday against a base near the town of Baga on Lake Chad, setting off fierce gun battles that killed 20 Nigerian and five Chadian troops, the sources said.
"The terrorists killed 20 Nigerian troops and five Chadian soldiers in the intense fight in which soldiers killed 47 of the terrorists," a military officer told Agence France Presse.
The head of a local anti-jihadist militia confirmed the military death toll and put ISWAP losses at "more than 40".
In a statement on Monday, the Multinational Joint Task Force (MNJTF) said 10 jihadists and a soldier were killed at the base while five troops were injured.
The MNJTF is a five-nation anti-military force headquartered in the Chadian capital N'djamena, comprising troops from Nigeria, Niger, Chad, Cameroon and Benin set up to fight jihadists in the Lake Chad region.
The military is known to downplay its losses in the fight against the jihadists.
The sources said that the jihadist raid on the base was repelled and the fleeing fighters were then met by a convoy of special forces bringing supplies from the regional capital Maiduguri.
"They ran into special forces who had been alerted by the troops in the base and more of the terrorists were killed in a brief encounter," a second military officer said.
ISWAP on Wednesday claimed that it had killed 15 soldiers in clashes near Baga.
The MNJTF base located four miles from Baga has been repeatedly attacked since 2014.
In December last year, ISWAP seized Baga and the base in an offensive that left several soldiers and militia fighters dead.
Although the MNJTF base was reclaimed weeks later, Baga and a separate naval base on Lake Chad remain under ISWAP control, according to locals and security sources.
The decade-long jihadist campaign of violence has killed some 27,000 people, displaced more than two million, and spilled into neighbouring countries.
ISWAP broke away from the main Boko Haram jihadist group in 2016 due to ideological differences.