This article presents the results of an extensive questionnaire survey focused on changes in the transport behaviour of the population of the Czech Republic immediately after the government’s announcement about the measures implemented to prevent the spread of COVID-19. The questionnaire aimed to determine the changes in the use of the mode of transport for regular travel to work, school, or for shopping, as well as to determine the changes in the frequency of these travels according to monitored socio-demographic groups of inhabitants and specified size groups of settlements. This article contains a statistical evaluation of these changes in the transport behaviour of the population using sophisticated statistical tools. A method for estimating the number of passengers in public transport using a linear regression model based on the data from conducted transport behaviour survey is proposed . In this paper, the Data envelopment analysis (hereinafter referred to as DEA method) within the case study in the South Bohemian Region is also used to determine whether the COVID-19 measures have reduced the efficiency of public transport.