Sunday's clashes, sparked by a recent attack on a church in southern Egypt, were the worst sectarian violence since the uprising that ousted Hosni Mubarak in February.
The MENA news agency did not say whether those arrested were Christians or Muslims.
Egypt's state television said authorities have stepped up security at vital installations in anticipation of renewed unrest, deploying additional troops outside parliament and the Cabinet.
The rioting in downtown Cairo had lasted until late into the night, bringing out a deployment of more than 1,000 security forces and armored vehicles to defend the Nile-side state television building, where the trouble began.
The clashes spread from outside the TV building to nearby Tahrir Square, drawing thousands of people to the vast plaza that served as the epicenter of the protests that ousted Mubarak. On Sunday night, they battled each other with rocks and firebombs, some tearing up pavement for ammunition and others collecting stones in boxes.
At one point, an armored security van sped into the crowd, striking a half-dozen protesters and throwing some into the air. Protesters retaliated by setting fire to military vehicles, a bus and private cars, sending flames rising into the night sky.
After midnight, mobs roamed downtown streets, attacking cars they suspected had Christian passengers. In many areas, there was no visible police or army presence to confront or stop them.
Christians, who make up about 10 percent of Egypt's 80 million people, blame the country's ruling military council for being too lenient on those behind a spate of anti-Christian attacks since Mubarak's ouster. As Egypt undergoes a chaotic power transition and security vacuum in the wake of the uprising, the Coptic Christian minority is particularly worried about the show of force by ultraconservative Islamists.
Prime Minister Essam Sharaf, addressing the nation in a televised speech, said the violence threatened to throw Egypt's post-Mubarak transition off course.
"These events have taken us back several steps," he said. "Instead of moving forward to build a modern state on democratic principles we are back to seeking stability and searching for hidden hands — domestic and foreign — that meddle with the country's security and safety."
"I call on Egyptian people, Muslims and Christians, women and children, young men and elders to hold their unity," Sharaf said.
The Christian protesters said their demonstration began as a peaceful attempt to sit in at the television building. But then, they said, they came under attack by thugs in plainclothes who rained stones down on them and fired pellets.
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