Police fired tear gas near Cairo's Tahrir Square, heart of the 2011 uprising that toppled Hosni Mubarak, where thousands demanded Mursi quit and accused him of launching a "coup".
Angry youth hurled rocks at security forces and burned a police truck.
There were also violent protests in Alexandria, Port Said and Suez.
Opponents accused Mursi, who on Thursday issued a decree that puts his decisions above legal challenge until a new parliament is elected, of being the new Mubarak and hijacking the revolution.
"The people want to bring down the regime," shouted protesters in Tahrir, echoing a chant used in the uprising that forced Mubarak to step down. "Get out, Mursi," they chanted, along with "Mubarak tell Mursi, jail comes after the throne."
The United States, the European Union and the United Nations expressed concern at Mursi's move. Mursi's aides said the presidential decree was intended to speed up a protracted transition that has been hindered by legal obstacles but Mursi's rivals condemned him as an autocratic pharaoh who wanted to impose his Islamist vision on Egypt.
"I am for all Egyptians. I will not be biased against any son of Egypt," Mursi said on a stage outside the presidential palace, adding that he was working for social and economic stability and the rotation of power.
"Opposition in Egypt does not worry me, but it has to be real and strong," he said, seeking to placate his critics and telling Egyptians that he was committed to the revolution. "Go forward, always forward ... to a new Egypt."
Buoyed by accolades from around the world for mediating a truce between Hamas and Israel in the Gaza Strip, Mursi on Thursday ordered that a Muslim fundamentalist-dominated assembly writing the new constitution could not be dissolved by legal challenges.
"Mursi a 'temporary' dictator," was the headline in the independent daily Al-Masry Al-Youm.
Mursi, a fundamentalist whose roots are in the Muslim Brotherhood, also gave himself wide powers that allowed him to sack the unpopular general prosecutor and opened the door for a retrial for Mubarak and his aides.
The president's decree aimed to end the logjam and push Egypt, the Arab world's most populous nation, more quickly along its democratic path, the presidential spokesman said.
"President Mursi said we must go out of the bottleneck without breaking the bottle," Yasser Ali told Reuters.
Turbulence and turmoil
The president's decree said any decrees he issued while no parliament sat could not be challenged, moves that consolidated his power but look set to polarise Egypt further, threatening more turbulence in a nation at the heart of the Arab Spring.
The turmoil has weighed heavily on Egypt's faltering economy that was thrown a lifeline this week when a preliminary deal was reached with the International Monetary Fund for a $4.8 billion loan. But it also means unpopular economic measures.
In Alexandria, north of Cairo, protesters ransacked an office of the Brotherhood's political party, burning books and chairs in the street. Supporters of Mursi and opponents clashed elsewhere in the city, leaving 12 injured.
A party building was also attacked by stone-throwing protesters in Port Said, and demonstrators in Suez threw petrol bombs that burned banners outside the party building.
Although Washington praised Egypt for its part in bringing Israelis and Palestinians to a ceasefire on Wednesday, it expressed concern about Mursi's move.
"The decisions and declarations announced on November 22 raise concerns for many Egyptians and for the international community," State Department spokeswoman Victoria Nuland said in a statement. The United States has been concerned about the fate of what was once a close ally under Mubarak, who preserved Egypt's 1979 peace treaty with Israel.
The European Union urged Mursi to respect the democratic process, while the United Nations expressed fears about human rights.
"We are very concerned about the possible huge ramifications of this declaration on human rights and the rule of law in Egypt," Rupert Colville, spokesman for the UN Human Rights Commissioner Navi Pillay, said at the United Nations in Geneva.
"Another dictator"
"The decree is basically a coup on state institutions and the rule of law that is likely to undermine the revolution and the transition to democracy," said Mervat Ahmed, an independent activist in Tahrir protesting against the decree.
"I worry Mursi will be another dictator like the one before him."
Leading liberal Mohamed ElBaradei, who joined other politicians on Thursday night to demand the decree was withdrawn, wrote on his Twitter account that Mursi had "usurped all state powers and appointed himself Egypt's new pharaoh".
Almost two years after Mubarak was toppled and about five months since Mursi took office, propelled to the post by the Muslim Brotherhood, Egypt has no permanent constitution, which must be in place before new parliamentary elections are held.
The last parliament, which sat for the first time earlier this year, was dissolved after a court declared it void. It was dominated by the Brotherhood's political party.
An assembly drawing up the constitution has yet to complete its work. Many liberals, Christians and others have walked out accusing the fundamentalists who dominate it of ignoring their voices over the extent that Islam should be enshrined in the new state.
Opponents call for the assembly to be scrapped and remade. Mursi's decree protects the existing one and extends the deadline for drafting a document by two months, pushing it back to February, further delaying a new parliamentary election.
Explaining the rationale behind the moves, the presidential spokesman said: "This means ending the period of constitutional instability to arrive at a state with a written constitution, an elected president and parliament."
"This is not the remedy "
Analyst Seif El Din Abdel Fatah said the decree targeted the judiciary which had reversed, for example, an earlier Mursi decision to remove the prosecutor.
Mursi, who is now protected by his new decree from judicial reversals, said the judiciary contained honourable men but said he would uncover corrupt elements. He also said he would ensure independence for the judicial, executive and legislative powers.
Although many of Mursi's opponents also opposed the sacked prosecutor, whom they blamed for shortcomings in prosecuting Mubarak and his aides, and also want judicial reform, they say a draconian presidential decree was not the way to do it.
"There was a disease but this is not the remedy," said Hassan Nafaa, a liberal-minded political science professor and activist at Cairo University.
COMMENTS (8)
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All those who support Morsi are ignorant about the history of Muslim Brotherhood. Muslim Brotherhood is an organization funded and guided by Saudi Arabia and like minded states. Before the revolution in Egypt, Muslim Brotherhood had been successfully infiltrated by western trained moles like Morsi. Where ever Muslim Brotherhood is gaining power, they are anti Iran and pro-Israel. The innocent Revolutionaries have no idea how their campaign was highjacked. No wonder Morsi has suddenly become the regional spokesman for the USA and Israel, and no wonder Israel agrees to what Morsi says. The world will know better when the US troops land in Egyptian Sinai to protect Israel, strangle Hamas/Gaza and encircle Iran.
it seems the opposition of Brotherhood is too hasty in opposing anything and everything that comes their way. its only immature of them to do so.
Mursi has a strong party to back him up - and unless they oppose him, the Egyptians can do whatever they like in Tahrir Square, this Government is here to stay.
The reason he needed such supremacy is to streamline the transition from a liberal-Mubarak Egypt in to a conservative-Mursi Egypt... which makes sense. Otherwise, each good move that he makes could be "legally" blocked and opposed until all this revolution that Egypt recently witnessed will go haywire. Egyptians should be grateful to the Brotherhood that after over 50 years of sacrifices, they are giving Egypt a new Government.
Mursi is another dictator being supported by the west to oppress its people.
All the best wishes to Mursi - In Egypt, the courts and Army are Husni Mubarak's legacy, whereas Democratically elected Presidency is an outcome of the revolution - Mursi is taking decisions which are really really brave of him.
It will be interesting to see how the USA handles this. They have gone out of their way to bolster his image as crucial to Israel/Hamas and he turns around and makes himself into a Dictator. Supporting an Islamic Dictator is going to be a tough sale for Obama.
Pharaoh Mursi ,U have to understand what exactly UN expect from you . So better remain Mursi for smooth transition .
So if a "leading liberal" Mohamed ElBaradei had labelled Mursi as a pharaoh in his tweet, you found no issues in adopting an inadmissible headline of "‘pharaoh’ Mursi"? Such brilliance!