"Due to developments over the past two days, the Brotherhood has decided to join in Tahrir Square rallies only symbolically, so as to avoid a situation where thugs take advantage of the place and attack public and private property or instigate confrontations where people may be injured or even killed, as happened on several previous occasions," party Secretary-General Mahmoud Hussein said in a statement.
"The Brotherhood calls upon all movements, groups and parties participating in Tahrir Square demonstrations and in rallies in governorates all over Egypt to express protest in a civilised and peaceful manner commensurate with the great civilisation of the people of Egypt and Islam," Hussein said.
On Wednesday, the party had called for nationwide demonstrations outside the main mosques in the country's 27 provinces against the film.
Thousands had attacked the American embassy in Cairo on Tuesday against the film. The protest was followed by clashes between small groups of demonstrators.