The capture by paramilitary forces of Wad Madani, a strategic city in the country’s agricultural region, marks a watershed in the civil war that has upended life in the northeast African nation.

The swift takeover on Tuesday of a major city in Sudan’s agricultural breadbasket by the Rapid Support Forces paramilitary group has sent shock waves throughout the country, cast doubt on the might of its rival — Sudan’s army — and opened a new and potentially deadlier phase in the eight-month civil war that has devastated one of Africa’s largest nations.

It took the paramilitary group only four days to capture the city, Wad Madani, where tens of thousands of people had fled from the capital, Khartoum, about 100 miles northwest, when the war started in April. The fall of Wad Madani has sent them running again, and dealt a huge blow to the prestige of an army that had promised to protect them.

“Depression is an understatement about how we feel,” said Omnia Elgunaid, a 21-year-old international relations graduate who fled from Wad Madani to a village farther south on Tuesday. “People are devastated because they now feel unsafe everywhere in the country.”

The army confirmed in a statement on Tuesday evening that it had withdrawn from the city, and — in a highly unusual move — said it has started an investigation into why this defeat happened.

The army’s loss has raised questions about the future of its leader, Gen. Abdel Fattah al-Burhan, who is also Sudan’s head of state. It also heightens the risk, analysts said, that neighboring countries could be pulled into the war, and that foreign powers, such as the United Arab Emirates, already accused of fueling the war, will further intervene.

The latest dramatic turn in the war has confounded Sudanese citizens who now face the prospect of a Sudan ruled by a dreaded paramilitary force that has looted much of the capital and been accused of carrying out war crimes in the western Darfur region.

The war has already killed at least 10,000 people, though Sudanese health workers and United Nations officials say that is a vast underestimate.

Some 300,000 people have fled Wad Madani in recent days, according to the United Nations. Many of them, ill and hungry, left the city on foot and walked for hours to neighboring states as they dragged suitcases and sheets holding their meager belongings.

Civilian groups in Wad Madani said the paramilitary forces had robbed civilians of gold, money and cars and stopped some of them from leaving the city. The paramilitary group said it would help resume basic services and protect civilians.

Aid agencies have largely halted operations in Wad Madani and the wider El Gezira State, and the U.N. has moved its staff to calmer areas in the country’s east or across the border into South Sudan. Aid workers, who have made the city a hub for their efforts, are concerned about the prospect of looting of humanitarian supplies and warehouses.

“The Sudanese people have lived through eight months of horror and the humanitarian situation keeps getting worse,” said Sofie Karlsson, the spokeswoman for the U.N. Office for the Coordination of Humanitarian Affairs in Sudan. “When your only choice is to leave by foot with what you can carry, you know the conditions have hit rock bottom.”

Amid the tumult, there has been a sharp focus on the army’s battlefield tactics and its chief, General al-Burhan.

The army had an aerial advantage over the Rapid Support Forces and has used aircraft to attack their bases. But the paramilitary forces have fired back at them using antiaircraft missiles provided by the Russian Wagner group, according to American officials. The paramilitaries have also taken over large parts of Khartoum and the adjoining cities across the Nile, besides sweeping through cities in the western Darfur region.

In Rufaa, a town about 30 miles north of Wad Madani, the army used a shipping container to block the paramilitary forces from crossing a bridge, a desperate deterrence that failed to stop their advancement, residents said.

Experts say that part of the reason for the army’s recent setbacks can be traced to its history.

Under the former dictator Omar Hassan al-Bashir, the Sudanese army largely outsourced the task of ground fighting to tribal militias like the Janjaweed, the hated group that terrorized the Darfur region in the 2000s and later became the Rapid Support Forces.

Now that the army has to fight a grinding war in a vast nation, its weaknesses are quickly emerging, said Alan Boswell, the Horn of Africa director at the International Crisis Group.

“It was a highly politicized army, people were promoted often because of ideology and nepotism. It became very corrupt,” Mr. Boswell said. “The army has never had to fight a war like this before and has shown itself not fit for purpose.”

The fall of Wad Madani shows that the failures go all the way to the top of the army, said Kholood Khair of Confluence Advisory, a Sudanese research group.

“Something has gone terribly wrong within the top brass of the Sudanese Armed Forces,” she said. “It is something that even some of them don’t understand.”

The capture of Wad Madani could pave the way for the paramilitary group to launch new attacks on other major cities, including Gedaref in the east and Kosti in the south.

Buoyed by their success, the paramilitaries may now be seeking to foment a revolt inside the army, analysts say.

In a social media post on Tuesday, the R.S.F. commander, Lt. Gen. Mohamed Hamdan, said his forces would not “become the alternative army” — a comment that many observers saw as an attempt to undermine the army chief, General al-Burhan.

Whether General al-Burhan can hold onto his job, Mr. Boswell said, depends on whether other Sudanese generals are willing to make a potentially destabilizing leadership change, in the middle of a war, and run the risk of splitting their own ranks.

General al-Burhan is the main interlocutor with the army’s foreign backers, Mr. Boswell said, adding, “Other generals may need to assess whether removing him could hurt those connections.”

As the conflict enters a new phase, experts say there’s also a greater risk of foreign interference. These include neighboring countries such as Eritrea, whose autocratic leader met in September and November with Sudan’s army chief.

The United Arab Emirates has been giving weapons and medical support to the paramilitary forces, accusations that they deny. A destabilized Sudan would also be unsettling for Saudi Arabia, which lies across the Red Sea.

A wider regional conflict would be “a nightmare scenario not just for Sudan but for the world,” said Ms. Khair, the analyst.

For now, many Sudanese hope they can find food and shelter. On Wednesday, Ms. Elgunaid said that she woke up with a fever, but that none of the pharmacies in the village where she was were open. Phone and internet connections were slow and many people still slept in the open, she said.

“We have no idea what we will do next,” she said. “We all feel trapped.”