The outspoken leader of the separatist group has not been seen in public since September 14.
There was heavy military presence inside and outside the courtroom on Tuesday as Kanu was expected to show up to defend himself against charges of conspiracy and treasonable felony alongside fellow defendants: David Nwawuisi, Benjamin Madubugwu, and Chidiebere Onwudiwe.
The outspoken leader of the separatist group has not been seen in public since September 14 after the military's alleged invasion of his father's home in Umuahia.
While the three other defendants were present in court during the commencement of the case on Tuesday, Kanu's counsel, Ifeanyi Ejiofor, announced the appearance of the IPOB leader, but alleged that he is in custody of the government.
"The Nigerian Army invaded his house and killed 28 people. I do not even know if he is alive or dead. The soldiers are in a better position to tell us," he said.
The government has always maintained that Kanu has gone into hiding to avoid prosecution with other rumours circulating that he might have even escaped to the United Kingdom.
While condemning Kanu's failure to appear as a "a grave violation of the order of this court", the prosecution counsel, Mr. Shuaibu Labaran, urged Justice Nyako to revoke his bail and order the three sureties that facilitated his release to "show cause why the bail bond of N100m entered into by each shall not be forfeited or they be committed to prison."
Kanu was arrested by the Department of State Services (DSS) in 2015 and he spent two years in custody until he was granted bail on health grounds in April 2017.
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The bail was granted bail by Justice Nyako on Tuesday, April 25, with Senator Enyinnaya Abaribe, Jewish High Chief Priest, Immanuu-El Shalom Okabemadu and a Chartered Accountant resident in Abuja, Tochukwu Uchendu, signing his bail bond.
During the court proceedings, Senator Abaribe's counsel, Mr. Ogechi Ogunna, filed an application for the lawmaker to be discharged as Kanu's surety, an application that was turned down by the court.
Justice Nyako said the lawmaker's only options are to either produce the defendant, forfeit his N100 million bail bond or ask for time to produce Kanu.
Senator Abaribe's counsel opted to ask the court for more time to produce the IPOB leader despite claiming in his application that he "cannot reasonably be expected to produce the second respondent before this court at any subsequent date."
Justice Nyako later adjourned the case till November 20, 2017.