Juma Gul Gul, also known as Jumaghul, was granted an in-country special humanitarian visa on November 3, but received a second letter rejecting his application two weeks later, Home Affairs Department documents seen by AAP showed.
It stunned his friend and former mentor, Warren Stevens and his wife Jo, who had been handling the paperwork and application.
Mr Stevens had trained Jumaghul at a trade school in Afghanistan during his first tour in 2008.
The couple had first helped lodge a physical visa form, which they then struggled to get confirmation of when contacting the Home Affairs Department for updates, before an electronic one was submitted.
Unbeknownst to them, a third application from a legal clinic had also been submitted.
The department clarified to the couple that two applications had been rejected for administrative reasons, while the humanitarian visa he was granted remains active after AAP reported the rejection.
The home affairs and immigration minister's office didn't reply to a request for comment for the initial story.
Jumaghul worked as a tradie on a military base in Afghanistan, including areas sequestered for special forces soldiers, which showed he was trusted by Australian authorities, Mr Stevens said after receiving the rejection letter that was perceived as a revocation.
There were fears for his safety as the Taliban had been persecuting and killing Afghans who had worked with Western forces after retaking control of the country in 2021.
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