The march had been scheduled to take place Nov. 10, a day after the anniversary of Kristallnacht - the 1938 night of terror when the Nazis attacked synagogues and Jewish homes and businesses throughout Germany and parts of Austria.
The event - organized by the Young National Democrats, which is linked to the National Resistance, a neo-Nazi group - was condemned by Jewish leaders and Czech President Vaclav Klaus said it was a "politically and morally unacceptable act which dishonors the memory of the victims of Nazi crimes."
Organizers said the march was meant to protest the deployment of Czech troops in Iraq.
Prague City Hall originally banned the march on Oct. 4, saying it would incite "hatred and intolerance of citizens because of their nationality, origin and religious faith." That ruling was later overturned by Prague's Municipal Court over procedural issues.
The city appealed to a higher court. No ruling has been issued so far.
In the meantime, Prague authorities said they found the announcement of the march from Aug. 27 was not valid because the group legally did not exist until Sept. 13. They said the organizers would have to formally inform City Hall again.
That was done on Monday, and on Tuesday the march was banned for the same reasons as before, City Hall spokesman Jiri Wolf said.
Prague's Jews had said that if the march went ahead they would gather at the same time to commemorate victims of the Nazi pogrom and prevent the march from going through the Jewish quarter.