Nearly a week before the National Oceanic and Atmospheric Administration (NOAA) publicly backed Donald Trump over its own scientists, a top NOAA official warned staff against contradicting the president.

Staff were told to “only stick with official National Hurricane Centre forecasts if questions arise from some national level social media posts which hit the news this afternoon” in an agency-wide directive sent to National Weather Service personnel on 1 September.

This was hours after Mr Trump asserted with no evidence that Alabama “would most likely be hit (much) harder than anticipated”.

They were also told not to “provide any opinion”, according to a copy of the email obtained by The Washington Post.

A NOAA meteorologist said the note, understood internally to be referring to Mr Trump, came after the National Weather Service office in Birmingham contradicted Mr Trump by tweeting Alabama would “NOT see any impacts from the hurricane”.

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The Birmingham office sent the tweet after receiving a flurry of phone calls from concerned residents following Mr Trump’s message.

The agency sent a similar message warning scientists and meteorologists not to speak out on 4 September, after the president showed a hurricane map from 29 August modified with a hand-drawn, half-circle in black sharpie around Alabama.

“This is the first time I’ve felt pressure from above to not say what truly is the forecast,” the meteorologist said. “It’s hard for me to wrap my head around. One of the things we train on is to dispel inaccurate rumours and ultimately that is what was occurring – ultimately what the Alabama office did is provide a forecast with their tweet, that is what they get paid to do.”

An NWS spokesperson said: “NWS leadership sent this guidance to field staff so they (and the entire agency) could maintain operational focus on Dorian and other severe weather hazards without distraction.”

Late Friday afternoon, NOAA officials further angered scientists within and beyond the agency by releasing a statement, attributed to an unnamed agency spokesperson, supporting Mr Trump’s claims on Alabama and chastising the agency’s Birmingham meteorologists for speaking in absolutes.

That statement set off a firestorm among scientists, who attacked NOAA officials for bending to Mr Trump’s will.

”This looks like classic politically motivated obfuscation to justify inaccurate statements made by the boss. It is truly sad to see political appointees undermining the superb, lifesaving work of NOAA’s talented and dedicated career servant,” said Jane Lubchenco, who served as NOAA administrator under former president Barack Obama.

NOAA, which oversees the National Weather Service, is not the first agency in the Trump administration to publicly side with the president after he has doubled down on a widely disputed claim.

But the firestorm surrounding the president’s hurricane statements is unprecedented in the organisations' history, and threatens to politicise something that most Americans take for granted as an objective, if flawed, part of daily life: the weather forecast.

A NOAA official disputed the suggestion that the statement took sides, saying there was “no political motivation” behind it.

The official said agency leadership had considered making a statement for “a day or two” to clear up confusion. Acting NOAA administrator Neil Jacobs was involved in drawing up the statement as was the NOAA director of public affairs, Julie Kay Roberts, who has experience in emergency management and worked on the president’s campaign.

Donald Trump shows off map purporting to support false claim that Hurricane Dorian was heading for Alabama

The official said the statement called out Birmingham’s tweet because one NOAA hurricane forecast showed a 5 to 20 per cent chance of tropical-storm-force winds in a small part of Alabama.

“It was nothing against Birmingham, we needed to make sure forecast products reflect probabilistic guidance,” they said, referencing the extremely low odds for tropical storm-force winds.

Such wind speeds, between 39 and 74mph, rarely cause much damage or require advance preparation.

The NOAA statement made no reference of the fact that when Mr Trump tweeted that Alabama was at risk, the state was not in the National Hurricane Centres' “cone of uncertainty”, which forecasters use to determine where the storm is most likely to hit.

Alabama had also not appeared in the cone in the days before that.

The acting NOAA director briefed the president on Hurricane Dorian on 29 August using the forecast cone that the White House later adapted via sharpie marker.

The director of the National Hurricane Centre briefed the president on the storm’s likely track again on 1 September, shortly after his tweet about the threat to Alabama.

At other times, Mr Trump was briefed by individuals, including the White House homeland security and counterterrorism adviser, who lacked the meteorological expertise to interpret what they were showing.

“If the president had been briefed by someone who understands the forecast, he never would’ve mentioned Alabama,” the NOAA official said.

NOAA’s statement infuriated scientists, who worry the Trump administration is corroding faith in research and data.

“It makes me speechless that the leadership would put [Trump’s] feelings and ego ahead of putting out weather information accurately,” said Michael Halpern, a deputy director at the Union of Concerned Scientists. “If we’re politicising the weather what is there left to politicise? We’re seeing this kind of clamp down of scientists across the government, and it’s been an escalating trend.”

Royal Navy providing emergency service in Bahamas after Hurricane Dorian

In 2018, a survey of scientists at 16 federal agencies found a culture of fear and self-censorship in an administration that has sidelined scientific evidence, especially as it related to climate change, in favour of political expediency.

Keith Seitter, executive director of the American Meteorological Society, said: “The criticism of the Birmingham forecast office is unwarranted; rather they should have been commended for their quick action based on science in clearly communicating the lack of threat to the citizens of Alabama.”

One of the strongest reactions to the NOAA statement came from David Titley, an atmospheric scientist who served as the chief operating officer of NOAA under Obama.

“Perhaps the darkest day ever for leadership. Don’t know how they will ever look their workforce in the eye again. Moral cowardice,” he tweeted.

Others who weighed in on social media were also scathing in their response to NOAA’s decision to publicly defend Mr Trump.

“I have never been so embarrassed by NOAA. What they did is just disgusting,” Dan Sobien, president of the National Weather Service’s labour union, wrote on Twitter.

“Let me assure you the hard working employees of the NWS had nothing to do with the utterly disgusting and disingenuous tweet sent out by NOAA management tonight.”

A popular television broadcast meteorologist in Birmingham also came to the defence of his city’s National Weather Service team.

“The tweet from NWS Birmingham was spot on and accurate,” James Spann tweeted. “If they are coming after them, they might as well come after me. How in the world has it come to this?”

On Saturday, the National Weather Service leadership seemingly tried to address the outcry in an all-hands letter to its employees to thank them for their hard work during the hurricane.

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The letter, obtained by The Washington Post, assured employees they were valued.

“We want to assure you that we stand behind our entire workforce and the integrity of the forecast process, including the incredible scientific, technical and engineering skill you demonstrated for this event,” the NWS leadership wrote.

“We saw first hand that our integrated forecast process works, and we continue to embrace and uphold the essential integrity of the entire forecast process as it was applied by ALL NWS offices to ensure public safety first and foremost.”