Workers have been spraying the inside of three trams and two buses with different types of disinfectant nano-polymers.
After two weeks, officials will judge which one works best and then disinfect all public transportation vehicles and subway stations in the city.
Officials say conventional disinfectants only work for a limited time, but they believe the nano-polymers could be effective for up to 21 days.
The Czech Republic has 104 confirmed cases of the virus.
For most people, the new coronavirus causes only mild or moderate symptoms, such as fever and cough. For some, especially older adults and people with existing health problems, it can cause more severe illness, including pneumonia.
The vast majority of people recover from the new virus. According to the World Health Organization, people with mild illness recover in about two weeks, while those with more severe illness may take three to six weeks to recover.
In mainland China, where the virus first detected, more than 80,000 people have been diagnosed and more than 58,000 have so far recovered.