The cartoons, originally created by Danish artists, sparked worldwide controversy and protests, especially in Muslim countries, two years ago.
The posters depict Muhammad with a bomb on his head instead of a turban. The image is accompanied by words "Freedom is not for free".
The Ministry of Foreign Affairs has sharply condemned the affair.
"In his time, the prophet Muhammad didn't know what bombs were, it's complete ridicule. I view such posters as being an expression of intolerance and aggression on the part of the people who have displayed them," commented Minister of Foreign Affairs Karel Schwarzenberg.
"I consider it a sad fact that something like that has emerged in the Czech nation. It has nothing to do with the freedom of speech," added Schwarzenberg.
"According to our opinion, no action that aims at inciting religious hostility or that may obviously lead to such ends can be defended by making references to the freedom of speech and expression," explained the ministry's spokeswoman Zuzana Opletalová.
Currently, the issue is being investigated by the police. "Anti-extremism unit is handling the case and experts will be called on to offer their opinions," said the spokeswoman for the Brno police Andrea Procházková.
"Experts will be able to determine whether this can be considered a crime or not," added Procházková.
Source: Actualne (English) h/t JammieWearingFool