SCAF General Adel Emara, interrupting a live news conference, said he had "received a call now to say that a plot was uncovered today to burn parliament and there are now large crowds in Tahrir Square ready to implement the plan."
AFP reporters in Tahrir said there were no signs of tension there or on the square's outskirts, where a historic building containing national archives was destroyed and protesters were trying to save any surviving documents.
Emara said the army "does not use force against protesters" but qualified those in Tahrir as "people seeking to destroy the state... not the honourable people of the January 25 revolution."
But Emara did admit troops had beaten a veiled woman after having ripped her clothes to reveal her bra, sparking nationwide outrage.
In the picture and YouTube footage of the incident, the woman is sprawled on the ground, helmeted troops towering over her. One is seen kicking her, and later she appears unconscious, her stomach bared and her bra showing.
"Yes, this happened. But you have to look at the circumstances around (the incident)," Emara told reporters.
"We are investigating it, we have nothing to hide," he said.
The comments came as rights groups and dissidents slammed retired army general Abdelmoneim Kato -- an adviser to the military -- for saying some in Tahrir were "street kids who deserve to be thrown into Hitler's incinerators."
Presidential hopeful and former UN nuclear watchdog chief Mohamed ElBaradei said such statements showed "a deranged and criminal state of mind."
The Arabic Network for Human Rights Information denounced Kato's comments, saying they "incite hatred and justify violence against citizens."
Footage on social media networks of military police beating protesters, sometimes leaving them motionless on the ground, has caused nationwide outrage.
A group of newly elected parliamentarians on Monday announced a sit-in outside the Cairo Supreme Court, demanding an immediate end to the violence against protesters and an investigation.
By Monday afternoon, protesters and police hurled rocks and stones at each other over a wall erected by the army in a large boulevard off Tahrir Square.
The violence drew international criticism.
UN leader Ban Ki-moon accused Egyptian security forces of using "excessive" violence against protesters.
Ban is "very concerned by the resurgence of violence," said his spokesman Martin Nesirky.
US Secretary of State Hillary Clinton urged "Egyptian security forces to respect and protect the universal rights of all Egyptians."
British Foreign Secretary William Hague said the violence in Cairo was "inconsistent with the democratic process in which Egypt is now engaged."
And rights watchdog Amnesty International urged arms suppliers to halt transfers to Egyptian forces.
"It can no longer be considered acceptable to supply the Egyptian army with the types of weaponry, munitions and other equipment that are being used to help carry out the brutal acts we have seen used against protesters," said Amnesty's Hassiba Hadj Sahraoui.
A health ministry source said two people were killed on Monday, bringing the death toll from four days of fighting to 12.
In the early morning raid on Tahrir and its outskirts, demonstrators held their ground and several dozens milled about the square, brandishing banners denouncing the SCAF, AFP correspondents said.
One man held up a bloodied white shirt, which had reportedly been worn by the person killed at dawn.
Security forces built another cement wall on a street adjacent to Tahrir near the Institute of Egypt, the historic building housing priceless archives, many of which were destroyed in the latest violence when it was burned.
The institute for the advancement of scientific research was founded in 1798 during Napoleon Bonaparte's expedition to Egypt, and contained more than 200,000 precious documents.
The French foreign ministry demanded a thorough investigation into the blaze of what was considered Egypt's richest library, describing it as "a tragedy for world cultural heritage."
The street battles that erupted on Friday raged outside the parliament building and the headquarters of the government.
The violence overshadowed the count in the first post-revolution vote that shows Islamists in the lead.
The Muslim Brotherhood's Freedom and Justice party said it won 39 percent of votes in party lists, while the Al-Nur party -- which represents the hardline brand of Salafi Islam -- claimed more than 30 percent.
The military, which took power when Mubarak was ousted, has decided on a complex electoral system in which voters cast ballots for party lists, that will make up two thirds of the lower house of parliament, and for individual candidates for the remaining third.