Sources from Bashir’s family said on Wednesday that the deposed president was transferred to Kober prison in north Khartoum late on Tuesday.
Bashir was ousted by the military on April 11 after four months of protests over his policies. Since then, he had been under house arrest in the presidential residence inside the compound that also houses the defense ministry, Presstv Reported.
A prison source said Bashir was being held under tight security in solitary confinement.
Witnesses reported a heavy deployment of soldiers and members of the paramilitary Rapid Support Force outside the prison. "There are troops in vehicles mounted with machine-guns near the prison," a witness told AFP.
Kober prison, located on the east bank of the Blue Nile in a northern district of the capital, held thousands of political detainees under Bashir's 30-year rule and is Sudan's most notorious jail.
Despite the ouster of Bashir, protests have continued in Sudan with the leaders of demonstrations saying the unrest will not cease until the military council, which has overtaken power in Sudan since Bashir’s fall, hands power to a civilian-led authority ahead of elections.
On Monday, representatives of the Sudanese Professionals’ Association (SPA), which led the protests against Bashir, urged the dissolution of the military council and the formation of a new interim civilian council.
The SPA also issued a long list of demands for deeper and faster change to end repression and an economic crisis.
Doctors protest over lack of proper healthcare
Meanwhile, thousands of medical professionals took to the streets of Khartoum on Wednesday, calling for better healthcare services and basic human rights for the people.
They marched on the defense ministry, where protesters have been holding a sit-in since April 6.
"Now healthcare is for only some people because they have money," Abdulaziz Ibrahim, a protester and medical professional, said.
Chanting, "Revolution, Freedom and Justice," the protesters also slammed the increasing privatization of hospitals and medical care services.
"We see citizens suffering from lack of healthcare. The basic healthcare is not provided, and there is a lot of privatization," Dr Kanali, another protester, said.
Rebels in southern Sudan suspend hostilities
Also on Wednesday, Sudan's People's Liberation Movement-North, the country’s largest rebel group, announced that it would suspend hostilities in the southern states of Blue Nile and South Kordofan for up to three months in order to facilitate a transfer of power to civilians.
"As a goodwill gesture... to give a chance for an immediate transfer of power to civilians, I, commander of SPLM-N announce the suspending of hostilities for three months in all areas under its control until July 31, 2019," Abdulaziz al-Hilu, the leader of the rebel group, said in a statement.
The announcement comes days after Sudan's junta declared a nationwide ceasefire, which includes the war-torn regions of Darfur, Blue Nile and South Kordofan.
The SPLM-N had sought to overthrow Bashir and is seeking autonomy for Blue Nile and South Kordofan and a redistribution of wealth and political powers in the country.
Bashir, who took power through a military coup in 1989, is wanted by the Hague-based International Criminal Court on charges of war crimes, crimes against humanity, and genocide related to the war in Darfur. He rejects the charges.