An individual border force officer forgetting to send an email likely led to the refugee Hakeem al-Araibi spending almost three months in a Thai prison fighting off Bahraini attempts to have him extradited.

The head of the Australian Border Force, Michael Outram, told Senate estimates it was within his own organisation “where the process broke down” and Al-Araibi was allowed to board a flight to Thailand, unaware he was walking into the waiting arms of Thai and Bahraini authorities.

Outram apologised for the border force’s error but not for Al-Araibi’s detention, saying he couldn’t state that the error was the sole cause, or that Al-Araibi would not have been detained anyway.

“To offer an apology for him would say that the outcome … was entirely due to that error,” he said. “I can’t say that without speculating.”

Al-Araibi was arrested on 27 November last year when he arrived in Bangkok with his wife for their honeymoon. Thai authorities presented an Interpol red notice, issued at Bahrain’s request, as the basis for his arrest.

It would eventually be revealed that Bahrain was granted the red notice against Interpol’s policies which protect refugees from the country they fled. Al-Araibi has lived in Australia for five years and has refugee status based on his fears of persecution in Bahrain.

Earlier in Monday’s hearing, the AFP commissioner, Andrew Colvin, said the AFP – which acts as Interpol’s national central bureau in Australia – couldn’t access visa information and relied on the home affairs department to tell them if someone subject to a red notice was a refugee.

The department did not tell them Al-Araibi was a refugee until after Al-Araibi had been detained.

In his opening statement, Outram also took the opportunity to share specific information about his organisation’s involvement.

He said Interpol distributed Bahrain’s red notice on 8 November, and AFP sent it to the border force the following day.

The border force accessed the notice on 22 November, 13 days later but within the standard 14 days he said it took the department to get to each of the approximately 600 received each month.

“It ran details across home affairs systems … and an alert was created on the basis of the red notice.”

“When the ABF match a person to an Interpol alert, a true match notification advice is manually sent from the ABF to the AFP national central bureau and the Department of Home Affairs visa and citizenship group,” Outram said. “On this occasion [it] was not.”

This was an error, he said, by an individual officer who was “diligent” in his work but “neglected to send an email”. “This is where the process broke down.”

Outram did not blame the individual officer, but rather said the department was dealing with “legacy” systems which required almost entirely manual operation.

“Our officers work around the clock, managing huge volumes of transactions which require manual processes to bridge gaps between disparate IT systems,” he said. “Human error can and will continue to occur, but it is rare.”

On Tuesday the home affairs minister, Peter Dutton, agreed it was a “mistake”.

“The officers dropped the ball on this, but that’s a human error that’s been made and let’s put all of the hype aside,” he said.

“There’s no conspiracy that somebody is being denied information. It is a mistake that was made by an officer within border force and I think the commissioners Outram and [AFP commissioner Andrew] Colvin have dealt with it appropriately.”

Amnesty International Australia called for an independent investigation into the “monumental mistake”.

The error “cost a young man and his family months of heartache and could have cost them much more had he been sent back to Bahrain”, its spokesman, Tim O’Connor, said.

“The results of any investigation must be made public immediately, and systems put in place to ensure no other person will suffer as Hakeem and his family have. ‘Human error’ must never again result in someone’s life being endangered.”

Outram had also explained information must be individually downloaded for each red notice on the list, often in other languages, and the department must seek translations. “If this system was fully automated that would be nirvana for all of us,” he said.

The AFP’s deputy commissioner, Ramzi Jabbour, made particular note of the fact that Bahrain was granted its red notice on the same day the Thai consulate in Melbourne approved Al-Araibi’s visa, almost a full year after Al-Araibi was given refugee status.

He didn’t have the information which would allow him to call it anything but a coincidence.