Dr Evans Kidero and former members of his administration have been charged with conspiracy to commit an offence of corruption leading to the loss of Sh213 million.
Through lawyer James Orengo, Dr Kidero said the charges as framed relates to an offense that does not exist in law.
He is charged alongside former Nairobi county secretary Lillian Ndegwa, former chief finance officer Jimmy Mutuku Kiamba among others.
Other charges include abuse of office and fraudulent acquisition of public property.
The directors challenged the move to charge them together with the companies.
In the application, Dr. Kidero challenged the charges of conspiracy to commit corruption arguing that it was faulty.
The Nairobi Ex-governor also sought to be charged separately arguing that the charges were lumped together with an aim of embarrassing him.
The trial will start on May 6.