Abubakar Shekau censured the IS affirmation that Abu Musab al-Barnawi was currently pioneer.
Shekau blamed al-Barnawi for attempting to arrange an overthrow against him.
Boko Haram is battling to oust Nigeria's legislature and build up an Islamic State in the north.
In the most recent year and a half it has lost a large portion of the domain it had controlled subsequent to being pushed back by a hostile by the powers of Nigeria and its neighbors.
Shekau was last gotten notification from in a sound message last August, saying he was alive and had not been supplanted - an IS video discharged in April said the same.
In a 10-minute sound message in both Arabic and Hausa, Shekau seemed to separate Boko Haram from IS, yet at the same time called its pioneer Abu Bakr al-Baghdadi "caliph".
He said that some in Boko Haram had halted him speaking with al-Baghdadi.
"I was requested that send my belief system in keeping in touch with the caliph however it was controlled by a few people so as to accomplish their own particular narrow minded interests," he included, depicting an overthrow endeavor against him.
He said he had sent eight distinct letters to IS pioneers yet they didn't follow up on them, just to hear the news that he had been supplanted.
He then portrayed al-Barnawi and his adherents as polytheist.
Boko Haram has part before yet this is the most genuine division to date.
Abubakar Shekau's upheaval obviously demonstrates that there are profound contradictions, which could decipher into conflicts between the troopers faithful to the two pioneers.
It is additionally an indication of the shortcoming of the gathering, perhaps portending a consequent breakdown.
Military authorities say the split means that the gathering is breathing its last.
Be that as it may, some security experts alert that the inward wrangling could make it all the more savage and eccentric.
Nigeria and the other provincial powers will now need to make this factionalism advantageous for them.
Shekau had been blamed for storing sustenance and ammo furthermore of heading out IS military guides.
BBC's Abuja authority manager Naziru Mikailu says this split is prone to majorly affect the way the gathering works and could be a defining moment in the battle against the agitators.
Shekau assumed control as the gathering's pioneer after its originator, Muhammad Yusuf, passed on in Nigerian police care in July 2009.
Under his initiative Boko Haram turned out to be more radical, did more killings and swore constancy to IS in March 2015.
In various recordings, Shekau provoked the Nigerian powers, praising the gathering's rough demonstrations, including the snatching of the more than 200 Chibok schoolgirls in April 2014.
Nigeria's armed force has guaranteed to have executed him on a few events, and he has not showed up in a video since Boko Haram adjusted itself to IS.
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