On Monday Egypt's interim prime minister Essam Sharaf ordered the new governor of Qena to stop work for three months so life can return to normal at the city.
Qena citizens have entered their tenth day of protest, demanding that newly-appointed Christian governor Emad Mikhail be replaced. He is criticized for his links to the toppled regime.
A sit-in has been staged in front of the governor's building since Saturday 16 April, when protesters blocked the railway.
Mikhail was preceded by governor Magdi Ayoub, also Christian.
The efforts of the ruling Supreme Council of the Armed Forces and the government had failed to solve the crisis as demonstrators insisted on their demands.
In a statement to state-run TV, quoted by Middle East News Agency, Sharaf said he commissioned Qena governorate's general secretary, Maged Abdel Karim, to take charge temporarily.
He urged citizens to return to normality in respect of the right of residents of Qena and neighboring cities to access services.
A number of Qena protesters say they do not object to Mikhail because of his religion, but rather due to his involvement in killing pro-democracy protesters during the 25 January revolution, which brought down the regime of former president Hosni Mubarak.
But Mikhail, who previously served as assistant to the Giza security chief, denied involvement. He said he is ready to be tried if found to have participated in the killings.