Mohamed Abdulnasir Sheikh who appeared before Milimani Senior Principal Magistrate Peter Ndwiga was accused of allowing a defective bus to operate.
He was also indicted for failing to keep records of his drivers of the bus company.
He however denied the charges and has now been remanded at the Muthaiga Police Station to await preparation of fresh charges before a Narok court.
Sheikh was arrested on Sunday following the tragic bus accident last week and the police have impounded three buses belonging to the company.
The arrest came after Transport Cabinet Secretary Michael Kamau said that the company should be held responsible for the accident.
Kamau has stated that the government will use the accident as a basis to ban passenger vehicles from travelling at night in order to reduce accidents on the roads.
President Uhuru Kenyatta also put drivers and owners of PSVs on notice that they would be held responsible for the deaths of their passengers.
Inspector General of Police David Kimaiyo also stated that traffic officers implicated in a Public Service Vehicle bribery cartel are being investigated.
He stated if it is ascertained they are involved in corruption which has compromised road safety leading to accidents that have left many maimed or dead, they will be dealt with in accordance with the law which also includes dismissal from the Police Service.