Mr Mohammed Ali Ahmed was remanded to allow for further interrogation by the Anti- Terrorism Police Unit (ATPU) on the alleged scam.
He will be charged alongside two senior officials at the National Registration Bureau (NRB) Ms Linet Nyamboke Omare and Ms Joyce Kwamboka.
The two NRB employees were separately ordered to be reporting to the ATPU offices.
Mr Ahmed appeared before senior resident magistrate Ms Hellen Onkwani on Wednesday, while Ms Nyamboke and Ms Kwamboka appeared before senior principal magistrate Charity Oluoch.
10 COUNTS OF FORGERY
They all denied 10 counts of forgery filed against them by the Director of Public Prosecutions (DPP) Keriako Tobiko.
Besides reporting to the ATPU offices, the two NRB employees were orderd never to go any where near their offices to avoid interfering with the witnesses.
The three are alleged to have committed the alleged forgeries within a span of five years between 2012 and 2016.
Ms Nyamboke and Ms Kwamboka denied charges of altering registration documents which had been issued to refugees from Ethiopia , Somalia , Congo, Sudan and Rwanda.