The arrest warrant was issued on a motion filed by the prosecution counsel, after Onnoghen failed to show up in court on Wednesday.
Onnoghen is standing trial before the CCT over allegations of fraudulent declaration of assets.
The CCT has also ruled that Onnoghen be arraigned physically for trial on Friday.
A directive was also issued to the Department of State Services (DSS) to effect the arrest of the suspended CJN.
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