The desperation on the faces of tens of thousands of people in Afghanistan while they attempted to escape as the country came under Taliban rule was broadcast across the world.

As the US-led coalition fled the country in August 2021, the chaos outside Kabul airport intensified. Entire families gathered outside, hoping for a spot on an airlift, and more than 180 people in the crowd were killed in an Islamic State-led suicide attack.

An aid worker, Zemari Ahmadi, was later erroneously struck by an American drone two miles away, killing him and nine others – including seven children, one only two years old.

But as all this unfurled, email inboxes in Whitehall were clogged with a separate issue: dogs and cats.

The extent of this fixation can be revealed for the first time after hundreds of emails were released as part of an employment tribunal case brought by Josie Stewart, following her dismissal from the Foreign Office (FCDO) after she blew the whistle on a catalogue of failures about the Kabul withdrawal.

As part of her successful case against unfair dismissal, which on Tuesday was upheld by a panel of three judges, hundreds of secret and sensitive documents were disclosed during the hearing.

It was no surprise that government lawyers tried to hold the case behind closed doors, as it lifted the lid on questionable Whitehall decision-making.

Government emails about the animal charity Nowzad and its media-savvy founder, Pen Farthing, a former marine, ran to more than 250 pages.

Stewart, who worked in the Afghanistan crisis team, lost her job after her security clearance was removed when a BBC journalist mistakenly revealed she was the source of leaked emails.

Stewart claimed she spoke to the BBC in the public interest to corroborate another FCDO whistleblower’s account of the chaotic withdrawal after his version of events was challenged by politicians and senior civil servants. She said she leaked emails, which suggested Boris Johnson was involved in fast-tracking Nowzad for evacuation, to show the government’s priorities were warped after the then prime minister dismissed the claim as “total nonsense”.

Emails disclosed in Stewart’s case raise fresh doubts about Johnson’s assertion. They also reveal there was opposition across Whitehall to giving any special treatment to Farthing’s animals and staff.

An email from a senior environment official on 23 August 2021 referenced press reporting of “the prime minister’s decision to grant visas to Nowzad staff”, without correction. It also noted the decision came with a “significant risk of critical comparison with the government’s approach to allowing Afghans to seek refuge in the UK”.

On the same day a No 10 email urged the Ministry of Defence to shut down press reports that the department was blocking Nowzad from charting a private flight from Kabul.

At 1.33am on 25 August the then defence secretary, Ben Wallace, tweeted that Farthing’s staff had been cleared for evacuation, and that “if he arrives with his animals we will seek a slot for his plane”, but that “no one has the right in this humanitarian crisis to jump the queue”.

Hours later at 9.18am, Helen Bower-Easton, the then FCDO communications director, said Wallace’s tweets had caused a flap in Downing Street. Under the subject line “URGENT – Pen Farthing & dogs” she wrote: “Major No 10 comms concerns about Def Sec commitment overnight that we will get the Nowzad dogs out – don’t want to look like we are prioritising animals over people.”

This sparked a long email chain. At 9.25am Lesley Craig, the then head of the Pakistan and Afghanistan department at the FCDO, replied saying: “Hopefully we’re not looking to prioritise animals over people at risk from the Taliban.”

An official from the MoD emailed at 10.21am saying of Farthing “If he turns up with the dogs then the dogs are not coming.”

Philip Hall, who was in charge of the FCDO’s evacuation crisis centre, said Nowzad staff were not considered vulnerable enough to qualify for evacuation. At 10.28am he emailed: “As SRO [senior responsible officer] for the LOTR [Leave outside the rules] scheme I consider they are not with the agreed priority cohorts, including extreme vulnerability.”

But at 11.22am Hall added: “It is open to the PM to instruct that Nowzad should now be called forward, despite not being within the criteria.”

At this point there is confirmation that No 10 was asked to make a decision on Nowzad by the then foreign secretary, Dominic Raab, and the then national security adviser, Stephen Lovegrove.

After speaking to her boss, Rachel King, who was Raab’s deputy principal private secretary, said: “Nowzad are in the cohorts approved by ministers as candidates for LOTR.”

Nigel Casey, who was the government’s special representative on Afghanistan, then intervened to confirm Downing Street had been asked to decide on prioritising Nowzad.

Casey would later tell a committee of MPs that the idea Johnson was involved in the decision was based on a faulty assumption by a senior official. He also claimed he had searched his emails and found nothing of relevance on the Nowzad issue.

But there was a relevant email. At 11.15am he messaged King to say Lovegrove was asked to “seek clear guidance for us from No10 asap on what they would like us to do. Stephen agreed to pursue this urgently.”

Shortly after, Lovegrove informed colleagues that Nowzad’s staff would be given priority after all, according to a 11.50am email from Thomas Drew, the FCDO’s then director general of defence and security.

Hall, now, overruled, replied: “We’ll action this. There are 68 Afghan national in the Pen Farthing/Nowzad group. We shall security clear them with UKVI/Home Office, then issue Calls Forward.”

At 12.09pm the FCDO crisis team was told: “The prime minister has approved the Nowzad staff to be called forward.”

Later that day a sceptical Hall sought clarification on whether animals would be allowed on the flight: He wrote: “I am not SRO for animals … you must ask MOD whether they can carry animals, and if so, whether they would be putting animals’ lives over people’s lives. Tom Drew may then need to liaise with Stephen Lovegrove to establish the scope of the PM’s decision. (There’s a common sense answer, of course.)”

It was not until 28 August that Farthing confirmed to the FCDO officials that a flight with animals had safely left Kabul, but the staff who had been cleared for evacuation did not make the flight. They arrived later in the UK after fleeing Afghanistan by road.