The government has ordered all matatus to be washed daily to prevent the spread of coronavirus.
The seats must be disinfected in the morning and at night. Drivers and conductors will also undergo training on coronavirus.
Transport CS James Macharia said the Health ministry will conduct training at bus stops from 10am to 4pm.
"Public transport carries more than 90 per cent of the population. That is why we are giving public transport special focus and attention. A problem affecting the transport sector will have a great impact on all other sectors," he said.
This comes after the first coronavirus case in Kenya was confirmed on Friday.
The Transport ministry had on Tuesday summoned all matatu operators, six matatu associations and the SGR operators to discuss measures to be taken should the country report cases of coronavirus.
"We told them not to wait for the government to take action," Macharia said.
In the meeting, it was resolved that clean water should be available at bus stops and public toilets.
On Friday, Matatu Owners Association chairman Simon Kimutai told the Star on the phone that all operators have been instructed to ensure their vehicles are cleaned daily.
"We will do what we can to ensure passengers are safe," Kimutai said.
The chairman also said he had proposed that all touts handling money should be given gloves.
"We cannot afford to take any risks and everyone from the matatu crew and passengers should be safe," he added.
Kimutai also urged that all passengers to carry hand sanitisers.