"The Obama administration tried to say that if private funding was used to create and destroy embryos, federal funding could be used for the research, but it's all part of the same process," said Ron Stoddart, executive director of Nightlight Christian Adoptions, an agency that was one of the original plaintiffs in the lawsuit.
The agency organizes adoptions of unused stem cells created during in vitro fertilization so that these potential fetuses can be given to infertile couples.
Though Lamberth wrote in his ruling that he believed he was preserving the "status quo," the scientific community was shocked by the decision and lamented the breadth of impact it could have.
Dr. Francis Collins, director of the National Health Institutes, told reporters in a telephone briefing that "this decision has the potential to do serious damage to one of the most promising areas of biomedical research. It comes just at the time when we were really gaining momentum."
Susan Solomon, CEO of New York Stem Cell Foundation, told ABC News following the injunction that a ban has the potential to interfere not only with all federally funded research involving embryonic stem cells, but with many privately-funded labs and projects as well.
"This will stop research all over the country. Even if you have private funding, there's an impact because many of your collaborators could be federally funded and affected by this ruling," she said.
The NIH's consideration of future grants for this kind of research was initially blocked by the injunction. However, the NIH announced shortly after the ruling that projects in process would be able to continue.
Now that the injunction is temporarily lifted, grant consideration can theoretically resume, though the potential for the appeal to fail in court continues to loom over research, scientists said.
The fact that the injunction was ruled in the first place, and eventually could stand, highlights the danger of having medical research policy that is subject to the whims of the judicial system, Solomon said.
Now researchers are hoping for a lasting legislative change that will end the "on again, off again" of scientists' legal right to funding once and for all, Kamp said.
"Human embryonic stem cells have stood the test of time and are the current gold standard for human master stem cells. Losing the ability to compare other stem cells to this gold standard puts federally funded investigators at a scientific disadvantage," he told ABC News. "Overall, U.S. researchers will be at a competitive disadvantage compared to others in many parts of the world."