"If I have to do what is necessary to protect this nation I will, and I am afraid that I may be close to doing so," Mursi said in a speech at the opening session of a conference on women's rights.
"I will do so very, very soon. Sooner than those trying to shake the image of this nation think," said the Islamist leader.
The President's warning came two days after clashes had erupted between Brotherhood members and opponents demonstrating near the Brotherhood Guidance Bureau's headquarters in Moqattam. More than 200 people were injured in the clashes.
Mursi said he would not allow more Egyptian blood to be shed.
Describing the ongoing violence in several governorates between Muslim Brotherhood supporters and opponents, Mursi said, that it had "nothing to do with the revolution, but is violence, riots and attacks on public and private properties".
"All Egyptian blood is precious," Mursi tweeted today.
"Peaceful demonstration is a right for all," Mursi said, refusing to describe the events as part of the revolution, but instead termed them a "riot".
Mursi called on all political groups "not to provide any political cover for acts of violence and riot".
Mursi said that he "will not be happy" if investigations prove to "condemn some politicians".
"State bodies are recovering and are able to deter violators," the President said.
Mursi vowed to take action against politicians "disregarding their standing", adding that some used media outlets to instigate violence.
He stressed that instigators would not escape punishment.
"Instigators are participants in the crime," he said.
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