There has always been a way out for at least some of those dogs -- commonly referred to as "baladi dogs" in colloquial Arabic, which means a native Egyptian breed -- in the form of sending them abroad, to be adopted by families in the United States.
But a U.S. decision earlier this month to temporarily ban importing them from Egypt threw a wrench in the work of rescuers.
The Centers for Disease Control (CDC) cited multiple instances of dogs that contracted rabies in Egypt being brought to the U.S. in recent years as a reason for the decision.
CDC estimates 100,000 dogs are imported from countries at high-risk for rabies every year.
A spokesman for Egypt's agriculture ministry told ABC News the country had launched an investigation into the matter to find out what went wrong. But until the probe yields any tangible results, there is little room for rescuers to operate and save more dogs from abuse.
"This decision has completely paralyzed us," Ahmed Al Shurbaji, founder of HOPE-Egyptian Baladi Rescue & Rehabilitation, told ABC News.
"Given that it's difficult to export baladi dogs to European countries because most of the landlords do not allow dogs at their places, the U.S. has been the only door opened for us for many years," he said.
"Through my shelter, 103 dogs were exported for adoption in the U.S. in 2016, 2017 and 2018, but now I'm struggling to help more dogs because the shelter is overcrowded," he said. "Dogs must leave the shelter at some point and have a new home."
Dog rescuers interviewed by ABC News gave a grim outlook of the future of their rescue operations should the U.S. ban last for long. Egyptians are not fond of adopting baladi dogs, so there should be options, they believe.
The abundance of stray dogs has stirred some hot debates in Egypt over the past few years, with one Parliament member causing an outcry last year after floating the idea of exporting dogs to South Korea for meat consumption. There are more than 15 million stray dogs in the country, according to the agriculture minister's estimates.
Laila Fayek is an individual rescuer who earned wide acclaim in 2015 for saving Cleopatra, a baladi dog whose six puppies were murdered after being hit by a wooden stick in Alexandria. The dog was eventually sent to a family in the U.S.
She is now afraid other abused dogs could not be saved.
"Before the U.S. ban, seeing the relatively very few dogs who traveled and were happy was what pushed us to continue, because you really feel you made a difference in their quality of life and gave them a chance they would have never gotten in their home country," Fayek said.
"Egyptian baladi dogs are sadly, and by far, the most looked down upon dog breed, especially by Egyptians. Finding them homes in Egypt is almost impossible," she said.
The CDC said in May it will maintain the dog suspension "until appropriate veterinary safeguards to prevent the importation of rabid dogs from Egypt have been established," with dog rescuers admitting some Egyptians do not completely adhere to U.S. requirements.
Dr. Salah Hassan, a veterinarian who founded the American Veterinary Center, which has branches in the U.S. and Egypt, said part of the solution could be mandating a Rabies Titer Test for dogs before they are exported. It tests the effectiveness of the vaccine given to them.
"The U.S. should have required this test long time ago, as many countries do in Europe. They had defects in their regulations which they now want to address," he said.
Egyptian rescuers are hoping the CDC will speed up the process and set new regulations that can be followed. Otherwise, the fate of abused dogs would be up in the air.
"I am praying the CDC lifts the ban soon and applies reasonable and affordable policies for both rescue and personal dogs," Fayek said.