While women, children and the elderly can enter Egypt freely, though often after waiting days in testing conditions at a packed border, Sudanese men aged 16-50 must apply for visas.
The rule has led to a bottleneck in Wadi Halfa, 25 km south of the frontier and home to an Egyptian consulate, as businessmen, doctors and other well-to-do Sudanese pack hotels, schools and hospitals, and spill onto the streets.
Abdel Qadir Abdullah, Sudan's consul in Aswan, said on Sunday that as of five days ago, 6,000 passports were awaiting visas in Wadi Halfa and that Egypt's foreign ministry had sent reinforcements to speed up the process.
With Khartoum's airport shut, tens of thousands have fled by road to safer areas outside the capital, and across the country's borders.
At least 64,000 people have crossed into Egypt, according to government figures, already home to an estimated 4 million Sudanese and a country where many families have connections.
To do so they have crammed onto buses and trucks, paying as much as $500 each to be taken to the border posts of Arqeen to the west of Lake Nubia and Qustul just north of Wadi Halfa, and on to Egypt.
The sleepy, low-rise town, has become a vast waiting area for adult men seeking visas, and families who do not want to be separated from their kin.
The ministry said last week in response to questions about the border crossings that authorities had been working to facilitate evacuation of all nationalities from Sudan since the start of fighting, and to provide care for those crossing the frontier.
Some of those with the means to escape have left homes and possessions at the mercy of looters.
Khaled Ibrahim, a businessman in his 30s, was already in Wadi Halfa when he watched CCTV footage on his mobile phone of fighters rampaging through his house in Omdurman, shooting off door locks and burning cheques worth millions of Sudanese pounds.
He went back to collect some belongings and found his dog shot dead. He returned to Wadi Halfa to apply for his visa but was told to wait, so he sent his elderly parents to Egypt alone.
"How would they live and find ways to live without me?" he said, as he marked time in a coffee shop across the street from the Sudanese passport office, which takes in the documents and passes them on to the Egyptian consulate for processing.