CAIRO — A dispute over measures to counter the coronavirus in Khartoum, the capital of Sudan, has led to an open confrontation between the country’s military and political leaders, underscoring the fragility of the country’s transition to democracy.
The civilian prime minister, Abdalla Hamdok, announced on Thursday that he had fired the governor of Khartoum, Lt. Gen. Ahmed Abdoun Hamad, for defying a government order to cancel Friday prayers in Khartoum and its sister city across the Nile, Omdurman.
Like many African countries, Sudan has a relatively low incidence of coronavirus — 32 confirmed cases and five deaths from Covid-19, the disease caused by the virus — but officials fear that a larger outbreak would quickly overwhelm the country’s dilapidated health system.
But General Hamad refused the prime minister’s order, saying in a statement issued by his office hours later that he intended to remain in his position — an unusually public act of defiance that exposed a growing rift inside the ruling Supreme Council, which is composed of civilians and army generals and is supposed to lead the country toward democratic elections in 2022.
A year ago, tens of thousands of protesters massed at the gates of the army headquarters in Khartoum in euphoric scenes that forced the ouster of Omar Hassan al-Bashir, their despised dictator of three decades. The impassioned hope of that moment was captured in an image by Yasuyoshi Chiba, a photographer with Agence France-Presse, that on Thursday won the coveted World Press Photo of the Year award.
But that heady optimism has been tempered in recent months by political instability, economic collapse and flashes of violent turmoil that have unsteadied the trajectory of a country still struggling to emerge from the shadow of Mr. al-Bashir’s harsh rule.
Mr. Hamdok, a former senior economist with the United Nations, has struggled to hold his ground against army generals who have seized control of key policy portfolios, including the economy and peace talks with anti-government rebels in the south of the country, and in the restive western region of Darfur.
Last month Mr. Hamdok survived an apparent assassination attempt after an explosion hit his motorcade. No group claimed responsibility for the attack, but Mr. Hamdok’s supporters blamed it on military rivals they said were colluding with former officials from the al-Bashir regime. “There are people who are trying to target the gains of the Sudanese revolution,” Faisal Mohamed Saleh, the country’s information minister, said afterward.
The coronavirus crisis has exacerbated those tensions. After a jump in confirmed cases this week, the government canceled Friday prayers and announced a three-week lockdown set to take effect on Saturday.
In defiance of those orders, a group of protesters massed outside the army headquarters on Thursday to call for the ouster of Mr. Hamdok’s government. “No to the government of hunger,” read one sign.
Hours later, as the confrontation with the Khartoum governor, General Hamad, unfolded, senior Sudanese civilian officials contacted Western officials and local journalists to warn that they feared the military would use the coronavirus lockdown to seize power while the outside world was distracted by the public health crisis.
An official with an international body in Khartoum, speaking on the condition of anonymity to speak freely about his confidential conversations with government officials, said civilian leaders were at odds with the army chief, Lt. Gen. Abdel Fattah al-Burhan, whom they claimed was backed by oil-rich Qatar and by neighboring Egypt.
Mr. Hamdock’s transitional government operates under the Sovereign Council, which is headed by General al-Burhan.
Qatar has previously backed Islamist groups inside Sudan, while Egypt is jockeying for position in the region as part of a dispute with Ethiopia over a giant hydroelectric dam under construction on the Nile. Egypt’s president, Abdel Fattah el-Sisi, has welcomed General al-Burhan to Cairo but stressed that he supports Sudan’s transition to democracy.
Several Western officials, though, said there was little sign of an imminent power grab. A senior United States official, speaking on the condition of anonymity to discuss confidential assessments, said Sudan’s jittery civilian leaders, whose popularity has tumbled in recent months as the economy has plunged, had so frequently warned of a possible coup in Khartoum that they had become akin to the boy who cried wolf.
A Western official based in Sudan did describe Khartoum as being awash with rumors of a coup to be carried out under the cover of the coronavirus but said there were no concrete signs of any upheaval.
In an email, Ambassador Donald Booth, the U.S. special envoy for Sudan, said the Trump administration stood behind Mr. Hamdok’s transitional government.
“We recognize it represents a compromise between civilians and security forces, both of which were instrumental in ending the dictatorship of Omar al-Bashir,” Mr. Booth said, adding that the government “now needs to protect the Sudanese people from the Covid-19 pandemic.”
Civilian officials, whose power rests in large part on being able to rally popular support in the streets, have said the coronavirus has put them at a disadvantage since they now could not mobilize supporters lest they risk spreading the virus.
Sudan’s power struggle is complicated by tensions inside the military. Diplomats and analysts say that General al-Burhan is jockeying for supremacy with Lt. Gen. Mohamed Hamdan, the ambitious leader of a notorious paramilitary unit, the Rapid Support Forces, that massacred dozens of people, in a storm of shooting and mass rape, during a violent clear-out of protesters in June.
The regular military has long chafed at the power of General Hamdan, who controls a private business empire and has openly signaled his ambition to rule. In a sign of just how tangled the alliances and rivalries are within Sudan’s leadership, General Hamdan is now politically aligned with the civilian leaders whose supporters his troops massacred last summer.
Further complicating matters, former Bashir loyalists inside the security forces flexed their muscles in January when they mounted violent protests in Khartoum against their severance packages, highlighting the daunting task of restructuring Sudan’s hydra-headed security apparatus.
Public patience with the jostling between military and civilian leaders has worn thin as Sudan’s economy struggles.
An anticipated boost in foreign aid since the ouster of Mr. al-Bashir has failed to materialize. The United States still lists Sudan as a state sponsor of terrorism, stifling investment; widespread shortages of food, fuel and hard currency have resulted in hardship.
Many Sudanese line up for hours to buy a loaf bread or to get fuel for their cars; others have fled abroad. On Wednesday more than 50 migrants from Sudan and Eritrea disembarked in Libya’s capital, Tripoli, following a failed attempt to cross the Mediterranean to Europe, the United Nations said.
The coronavirus adds to those woes. On Thursday, Michel Yao, a senior official with the World Health Organization, warned that Africa could face a dramatic surge in infections in the coming months. In the worst-case projections, Mr. Yao said, the number of cases on the continent could shoot up from thousands to 10 million within the next three to six months.
Abdi Latif Dahir contributed reporting from Nairobi, and Eric Schmitt from Washington.