The Sh2 billion project has not been completed since May 2012.
The 26-storey complex in Upper Hill will be known as Umoja House.
Churches are aggressively pouring billions of shillings into Kenya's property sector.
The houses in the first phase will be sold to civil servants.
The 170-room City Lodge Hotel will be situated within Two Rivers Mall on Limuru Road.
Phase one and two of the project, comprising 850 housing units are completed and fully sold.
The new houses will be built using the Expanded Polystyrene (EPS) technology.
The Sh4.5 billion project will be completed in the next two years.
The facility is expected to boost power supply to the port to 132Kv from 11Kv.
The project has been in the pipeline since 2008.