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Defence Secretary Ben Wallace has rejected claims the UK government blocked a flight to rescue staff and animals from a shelter in Kabul.
Mr Wallace said he was not prepared to prioritise animals ahead of the evacuation of people "in real danger".
Paul "Pen" Farthing accused the Ministry of Defence of cutting him off after supporters raised funds for a cargo plane.
But Mr Wallace said he couldn't push them through Taliban checks or crowds.
Mr Farthing founded the Nowzad animal shelter in the Afghan capital, rescuing dogs, cats and donkeys after serving with the British Army in Afghanistan in the mid-2000s.
Mr Wallace said he had been offered a route out of Kabul as a British passport holder but if the cargo plane landed it would be waiting "hours and hours" for him and his staff to get through thousands of people queuing to escape the country.
"This is about whether the people who work for him and his rescue pets or animals can make it through the Taliban checkpoints, the crowds, the people in front of him in the queue," he added.
"Thousands and thousands of people, some of whom are under really, really direct threat, very dangerous threat because of what they did during the last 20 years, and they have a right to get on a plane as much as anyone else.
"So therefore our priority is getting those people processed and I simply can't push those people out of the way to allow through some of those other cases."
Mr Farthing hit back, telling Mr Wallace on Twitter: "You picked on the wrong person to back down. I served 22 years as a Royal Marine. We don't quit."
In another tweet, he added: "I have been left to fend for myself in Kabul...22-year Marine left behind lines...neither my staff or animals will now get out."
But Mr Wallace told Sky News: "I'm not prepared to prioritise pets over people.
"It is just not going to be the case that I will prioritise them over the men, women and children that we see in desperate need at the gate. I regret that but I don't believe the Taliban's main point of target will be his workforce and indeed the pets and the animals he is looking after compared to some of those other people desperate in front of the queue."
The defence secretary said Mr Farthing's staff had been offered a route out of Kabul but he could not guarantee they would be processed on to aircraft "in this window".