President Omar al-Bashir, who has ruled Sudan with an iron fist for three decades, has been overthrown and is being held by the military.
The country's defence minister told state television had been arrested and that a military council would be running the country for a two-year transitional period, with elections to follow.
But the main organiser of protests against al-Bashir rejected the minister's statement and called for demonstrations to continue.
Sources told Reuters that the Bashir was at the presidential residence under "heavy guard" while a son of Sadiq al-Mahdi, the head of the country's main opposition Umma Party, told al-Hadath TV that the former president was under house arrest with "a number of leaders of the terrorist Muslim Brotherhood group."
Omar Saleh Sennar, a senior member of the Sudanese Professionals' Association (SPA), told Reuters they would only accept a civilian government made up of opposition figures. He added that the group was still waiting for a statement by the army.
"We will only accept a transitional civilian government composed of the forces of the Declaration of Freedom and Change," he said.
Sudan's state news agency SUNA reported that the country's security service had released all political prisoners after Bashir's step down from power.
On Thursday morning, anti-government protesters marched through the streets of Khartoum chanting anti-Bashir slogans.
Protesters outside the defence ministry chanted: "It has fallen, we won."
Later in the day, soldiers were seen storming the headquarters of Bashir's Islamic Movement by Reuters witnesses.
Who is Omar al-Bashir?
Bashir, a former paratrooper, seized power in 1989 after a coup. Bashir was indicted by the International Criminal Court (ICC) in The Hague after allegations of genocide in Sudan's Darfur region surfaced.
The United States placed Bashir's government in its list of terrorism sponsors for allegedly fostering Islamist militants. Because of that, Sudan was placed under extended periods of isolation since 1993 after Washington slapped sanctions four years later.
It is not yet known what will happen to Bashir.
Raising the price of bread will make you an enemy of the people
After 30 years in power, Bashir stepped down after anti-government protests escalated in the weekend. On Tuesday, clashes between soldiers trying to protect protesters and security personnel ended with 11 dead including six members of the armed forces.
Protests started in December after the government tried to raise the price of bread and an economic crisis lead to shortages in fuel and cash.
Russia's foreign affairs committee chief Konstantin Kosaciov condemned the coup in a Facebook post:
"I don’t try to judge who is right there and who isn’t. I recall my principled position of denying the scenarios of unconstitutional change of power in principle - whether in Ukraine, Turkey, Syria, Venezuela, or anywhere else. And those who commit such coups must understand the enormous risks they place in their country," he wrote.