Suspended Transport Cabinet Secretary Michael Kamau was charged with abuse of office and failure to follow procurement rules when he appeared before a Nairobi court on Thursday.
The CS pleaded not guilty and was released on a Sh1 million cash bail.
His co-accused, Nicholas Mburu Ng'anga, also denied the same charges and was released on similar terms, while the third accused, Kaka Matemu Kithyo, was released on a Sh600,000 bail by Senior Principal Magistrate Lawrence Mogambi.
Mr Kamau had appeared in court earlier on Thursday morning to face charges over graft allegations.
The CS, however, did not take a plea, after the magistrate handed him back to the Ethics and Anti-Corruption Commission (EACC) for processing.
On Tuesday, Mr Kamau failed to appear before a magistrate's court after the police failed to find him at his home in Nairobi.
Senior Principal Magistrate Lawrence Mogambi then issued a summons for him to appear in court on Thursday.
However, Mr Kamau moved to the High Court on Tuesday, just hours after he was summoned, in a bid to stop his prosecution.
He argued that the EACC lacked the necessary quorum to recommend charges against him.
Justice Mumbi Ngugi ruled that Mr Kamau should take a plea as planned but stopped the hearing of the case until a determination of the application to stop Mr Kamau's trial is made.
The CS, along with five others, is accused of not following procurement rules in awarding the tender for the construction of the Kamukuywa-Kaptama- Kapsokwony-Sirisia road.