At least 12 people were killed Sunday when clashes erupted between mostly Coptic Christian demonstrators and security forces outside the state television building in central Cairo, the Health Ministry reported.
State television said at least three soldiers were among those killed, who were shot dead. Dozens of people were injured, dpa reported.
Activists wrote online that several civilians attacked protesters, alongside army forces and military police.
Prime Minister Essam Sharaf said that the clashes were an attempt to create chaos in the country and ignite sectarian tension.
In a statement on his Facebook page, Sharaf urged Egyptians to remain united against extremist "vandalizing forces."
"The enforcement of law on everyone is the best solution to all of Egypt's problems," Sharaf wrote.
The clashes began when some demonstrators threw stones at army troops guarding the television building. Several cars and buses were set on fire.
Hundreds of mostly Christian demonstrators have been protesting for several days over the destruction of a church on September 30 in the southern Egyptian province of Aswan.
State television and radio employees were trapped inside the building Sunday after the army closed all doors and prevented anyone from leaving, witnesses told dpa.
Several roads around the area were closed by protesters, who prevented cars from passing.
During the protest, led by several bishops, the demonstrators burnt photos of the governor of Aswan, Mustafa al-Sayed, who had said that the church in the village of Marinap had been built illegally.
The protesters demanded that the Aswan governor be sacked and the church rebuilt.
In the southern city of Luxor, a group of protesters briefly blocked the city's main roads. However, the governor convinced them to leave after promising to resolve the issue of the destroyed church.
Christians account for around 10 per cent of Egypt's 80 million people, and tensions are not uncommon with the country's Muslim majority.
In March, 13 people were killed in sectarian clashes around the Cairo neighbourhood of Manshiyet Nasser, shortly after a church was torched in the village of Sol, south of the capital.