Organizers of the rally had planned to stage the demonstration at a square of the city, where Obama is expected to make speech, news reports said.
City clerks said they had proposed to the organizers of the rally to move the demonstration to another place, but had got no response.
Obama will arrive in Prague on April 4 and will leave on April 5. His agenda in Prague includes talks with the heads of 27 EU states. The Czech Republic holds the rotating EU presidency for the first half of the year.
Source: FOCUS Information Agency