The Egyptian Social Democratic Party blamed the interior ministry for the clashes at the Islamist group's headquarters in Cairo's Moqattam district.
"After the attacks on unarmed protesters [including women] and journalists, the police should have arrested the thugs [who initiated the attacks], especially after videos showed their faces clearly. But the police prefer to arrest victims rather than criminals."
The party "warned" the interior ministry against "defending members of ruling [political group] at the expense of the people."
The liberal Free Egyptians Party said the events proved the existence of "organised militias that follow orders from the Muslim Brotherhood."
The incident showed "the real ruler of Egypt is the Brotherhood's supreme guide [Mohamed Badie] and not President Mohamed Morsi."
The liberal Constitution Party, lead by Mohamed ElBaradei, condemned the "criminal assaults" by Brotherhood "militias" on political activists, journalists and photographers.
"Pushing citizens to kill other citizens shows the rule of law has collapsed. This is a dangerous phenomenon that has erupted since the president came to power," the statement said.
Police used tear gas and bird shot to disperse around 3,000 protesters at the Muslim Brotherhood HQ on Sunday. Dozens of protesters, including journalist Mohamed Rashad, were arrested.
Violence broke out on Saturday between pro- and anti-Muslim Brotherhood protesters after a meeting between Brotherhood Supreme Guide Mohamed Badie and Hamas leader Khaled Meshaal at the Brotherhood HQ.