About 30 protesters on Saturday evening disrupted the performance of the play "Our violence and your violence" by a Bosnian born, Croatian stage director Oliver Frljic, in a theatre in Brno, Czech Radio reported on Sunday.
A few protesters climbed onto the stage and formed a human shield to prevent the audience from watching the play while some booed and threw pieces of paper at the actors.
The protesters were eventually thrown out of the theatre by riot police.
After an hour-long break, the play was resumed and played until the end, Czech Radio said.
It noted that the play, which includes a scene where a Muslim woman is being raped by Jesus, had caused controversy in other countries as well.
The Czech Catholic Church has protested strongly against the play.
About a year ago, Frljic's play provoked protests in the Croatian coastal city of Split, and local police then arrested 18 people for disturbing the peace.
The play caused disputes also in Poland and drew negative comments from Sarajevo Archbishop Vinko Puljic and the Split Diocese in Croatia.
The Croatian Culture Ministry at the time issued a statement saying that "while respecting the artistic freedoms and aesthetic criteria of each artist, we believe that in creating and performing works of art one should bear in mind religious and ethnic feelings as well as the fundamental rights of every individual and social group."
Split County war veterans associations have sued Frljic and organisers of the Split festival where the play was staged for insulting their religious and ethnic feelings.