Abubakar Shekau spoke for nearly 20 minutes of a 27-minute video obtained by AFP on Friday, in a trademark pose in front of a sub-machine gun, flanked by two masked militant fighters.
Speaking in the local languages Hausa and Kanuri, as well as Arabic, Shekau said the recording was made on Thursday and that he was "in good health", contrary to claims he may be injured.
But he appeared subdued compared with previous appearances.
Criticising regional leaders, he singled out Cameroon's President Paul Biya, whose government on Wednesday said troops had killed 60 Boko Haram fighters and arrested 21 others in recent weeks.
Government spokesman Issa Tchiroma Bakary also said more than 5,000 civilian "hostages" had been freed in operations along the border with Nigeria from February 27 to March 7.
But Shekau said: "We fought along the Cameroonian border. You lied that you killed 60 of our fighters, that you arrested 20 of our men, that you freed 5,000 of your people.
"Paul Biya, is it that you can't live off lies? Is it with this that you are going to convince the West, your leaders? It is unfortunate. Be careful, Paul Biya."
Caliphate 'running smoothly'
Shekau was last seen on camera in a video message in December last year after Nigeria's military claimed it had flushed out Boko Haram fighters from its Sambisa Forest stronghold.
Troops, with the help of regional forces from Cameroon, Chad and Niger, as well as Benin, have since early 2015 managed to claw back most of the territory lost to the radical Islamists in 2014.
But Shekau insisted "our caliphate is running smoothly". The militant leader declared an Islamic state in northeast Nigeria in August 2014.
Despite its loss of territory and claims from the military it is on the verge of defeat, suicide bomb attacks remain a threat to civilians, particularly in the Borno state capital, Maiduguri.
At least two people were killed on Wednesday when four female suicide bombers detonated their explosives in the city.
Shekau said the group was "responsible for all the suicide explosions in Maiduguri and we will continue with them".
Boko Haram released another video on Monday showing the execution of three men said to be government spies. But the message did not feature Shekau.
The latest video ends showing militant fighters in combat fatigues with assault rifles and apparently confiscated Cameroon police and army uniforms.
One fighter speaks in heavily-accented French, lending weight to theories that Boko Haram has recruited from parts of Nigeria's Francophone neighbours.
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