A parliamentary committee has raised alarm over the management of the Cooperative Societies Liquidation Fund.
Pressure has been mounting on Raila to reconsider his support for Ruto's administration.
A whistleblower had in June raised concerns about the secret deal.
The recommendation for charges followed a series of investigations that took 3 months.
Sifuna has been under fire over his stand on ODM and UDA partnership.
The CS, however, noted that the deal boosted the Kenyan shilling against the dollar.
The CEO was forcefully taken from her house on July 15.
Nyutu has in recent months, courted controversy with her political standing.
SHA has been reviewing claims.
The accusation comes at a time when the Ministry faces numerous instances of land case delays.