In a few years, the US Centers for Disease Control and Prevention is hoping to be able to predict outbreaks like a forecaster might do the weather, following the launch of its new pandemic forecasting unit on Tuesday.

But thanks to legal setbacks for the Biden administration, including a ruling earlier this week by a Donald Trump-appointed judge in Florida, its attempts to fight them could be frustrated.

Judge Kathryn Kimball Mizelle on Monday ruled the CDC’s requirement for all passengers to wear masks on public transport was not lawful and should be immediately overturned.

The decision was greeted with a mixture of jubilation for some passengers, who ripped off their masks mid-air with whoops and applause, and anxiety for others.

The Biden administration has said it will appeal, but only if CDC decides masks are necessary beyond May 3.

Some experts believe it should do so either way, warning the judgment could set a precedent that could affect the government’s ability to fight the next outbreak.

“This is part of a broad-scale attack on the federal government’s capacity to protect public health,” said Wendy Parmet, a law professor at Northeastern University. “This ruling is dangerous.”

The decision is the latest setback to the federal government’s attempts to stem the spread of Covid-19 and mitigate its impacts through national regulations.

Last July an appeals court upheld a lower court’s decision that the CDC could not impose restrictions on the cruise ship industry, such as forcing passengers to maintain social distancing and running Covid-19 testing laboratories on board.

Two months later, the Supreme Court ruled the CDC did not have the power to ban property owners from evicting tenants in areas of high transmission who declared themselves in financial need. All six conservative justices said this power should lie with individual states rather than the federal government, while the three liberals disagreed.

At the beginning of the year, the Supreme Court ruled the Biden administration had overstepped the mark by trying to bring in a vaccine requirement for most private sector workers, stopping the move in its tracks. The court was split again on ideological lines.

Despite this, many legal and public health professionals were surprised by Monday’s ruling against the mandate because the enforcement of mask-wearing had appeared to be one of the few powers Congress explicitly gave the CDC.

The legal argument hinges on two sentences contained in the Public Health Services Act of 1944.

In the first, Congress allows the CDC, with the approval of the Health Secretary, to introduce rules designed to stop the introduction and spread of infectious diseases either into the US or between states.

In the second, it lists measures the CDC can take to do so: inspection, fumigation, disinfection, sanitation, pest extermination, destruction of infected animals or items and “other measures”.

Mizelle ruled masking qualified neither as sanitation nor one of these unnamed “other measures”.

Many legal experts were shocked. Lawrence Gostin, professor of global health law at Georgetown University, said: “If the CDC cannot prevent the transmission of diseases by use of evidence-based masking, then I can’t think of anything it can do.”

Others see it as a worrying sign that the culture wars that have raged in the US over the pandemic response, encompassing everything from mask-wearing to vaccinations, are now influencing legal judgments.

Tom Frieden, the former CDC director, said: “The issue is a broader philosophical issue: do we even recognise there are certain things we cannot do as individuals which are better off done as a society?”

Experts argue that any appeal could be a political mis-step, once more inflaming tensions around this sensitive subject. It could also be legally risky: if the appeal is lost, it would simply cement the precedent set by Mizelle and make it harder for the CDC to take similar action in the future.

Gostin said he backed an appeal, but warned: “The courts have been so rogue throughout this pandemic, you might get an appeals court that upholds it, which would be an even worse precedent.”

But for many inside and outside the administration, an appeal is essential given the fundamental authorities of America’s public health bodies are at stake.

Parmet said: “This decision ties the CDC’s hands at a time when we still do not know what the next few months will bring in terms of the pandemic and new strains. It is really important the administration pushes back.”