Mr Kanu's page was removed for repeated violation of its community rules, the social networking site told the BBC.
He had posted a video of a militia group attacking and killing cattle in a herders' settlement.
He also used the live broadcast to accuse herders of destroying farmlands in eastern Nigeria.
The conflict between herders and other groups is currently one of Nigeria's hottest political issues.
Mr Kanu leads the Indigenous People of Biafra (Ipob), which campaigns for independence for Nigeria's south-eastern region, where the ethnic Igbo people form the majority.
The herders are mostly from the northern Fulani community.
Mr Kanu, who also has British nationality, used his Facebook page as a key platform to communicate with his followers around the world.
The account was blocked on Tuesday.
'Suppressing the truth'
The militia carrying out the attack in the video he posted are suspected to be from the Eastern Security Network, which Mr Kanu set up.
A Facebook spokesperson told BBC Igbo: "In line with our rules, we removed Nnamdi Kanu's page for repeatedly posting content that break those Community Standards, including content that violated our rules on coordinating harm and hate speech."
Ipob says it will appeal against the ban, describing the action of Facebook "as not only baffling but too petty".
"We wonder why a global social media giant like Facebook would allow itself to be used by agents of oppression in Nigeria to suppress the truth," head of media Emma Powerful said.
Ipob is proscribed in Nigeria, which labelled it a terrorist organisation in 2017.
Nnamdi Kanu came to fame in 2009 when he started Radio Biafra and broadcast to Nigeria from London, using the platform to call for Biafran independence and urging his followers to take up arms against the Nigerian state.
Who are Ipob?
. Founded by Nnamdi Kanu in 2014
. Proscribed as a terrorist group by Nigeria in 2017
. The group wants states in south-east Nigeria, made up mainly of people from the Igbo ethnic group, to break away and form the independent nation of Biafra
. Mr Kanu was arrested in 2015 in Nigeria and spent more than a year-and-a-half in jail without trial on treason charges
. At least 150 Ipob members were killed by Nigerian security forces between August 2015 and August 2016, according to Amnesty International
. Mr Kanu, a British citizen, jumped bail and fled the country in 2017
Related stories: Separatist leader Nnamdi Kanu resurfaces in Israel
The Biafra secessionist movement in Nigeria
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