ABF Commissioner Michael Outram told a Senate estimates hearing that it should have told the AFP and Home Affairs officers that the refugee footballer was protected.
Australian Border Force officials have admitted their processes "broke down" and accepted responsibility for the detention of refugee footballer Hakeem Al-Araibi.
ABF Commissioner Michael Outram said the agency should have told Australian Federal Police and Home Affairs officers Mr Al-Araibi was protected by a humanitarian visa.
This would have prevented Thailand being alerted to an Interpol red notice issued against him.
"It is clear that human error occurred within the ABF process," Mr Outram told a Senate estimates hearing in Canberra on Monday night.
The AFP has also identified a "gap" in its handling of the case but attributed most of the blame to the Department of Home Affairs.
Mr Al-Araibi, a permanent resident of Australia, was arrested in Bangkok in November.
Bahrain requested a red notice against him over disputed allegations Mr Al-Araibi vandalised a police station, and also claimed he may have been travelling on false documents
The 25-year-old returned to Australia last week after spending more than two months behind bars, following a decision by Thai authorities not to pursue extradition proceedings against him.
The AFP has blamed a lack of access to visa records for its role in his detention, pointing the finger at Home Affairs officials for failing to inform them.
Interpol did not know Mr Al-Araibi was a refugee, and would not have issued the notice if they had been aware.
"It was issued in good faith by Interpol; they were not aware at the time of issuing it that he was subject to a protection visa," AFP Commissioner Andrew Colvin told the committee.
Bahrain requested the red notice on November 8 and the AFP - which hosts an Interpol office and has staff seconded there - told Australian Border Force officials the following day.
"At this time, neither the AFP nor the Australian Interpol NCB (National Central Bureau) was aware of Mr Al-Araibi's visa status," Mr Colvin said.
"Neither the AFP nor the Australian Interpol NCB can access this information; we rely on notifications from the Home Affairs department.
"The Home Affairs department provided Mr al-Araibi's visa status to the AFP on the 28th of November, the day after his detention in Thailand."
The AFP then referred his visa status to Interpol's legal affairs department, and Mr Al-Araibi's red notice was rescinded on December 1.
He returned to Melbourne on February 12, once the extradition case against him was finally dropped.
There is no legal obligation for Home Affairs to notify federal police about somebody's refugee status.
An AFP review uncovered the "gap".
On November 28, the day after Mr Al-Araibi was arrested in Thailand, an AFP officer emailed Home Affairs about his case.
Bahrain raised allegations with Interpol that the 25-year-old departed Australia on a suspected fake travel document.
An AFP employee raised the matter with Home Affairs.
Home Affairs advised the AFP officer that Mr Al-Araibi was travelling on a valid document, and also held a protection visa.
This was the first time the AFP was notified of Mr Al-Araibi's visa status.
However, the response from Home Affairs was not read.
The AFP employee had gone home and did not return to work until after Home Affairs provided separate advice about Mr Al-Araibi's protection visa.
The AFP insists this "gap" had no impact on Mr Al-Araibi's detention, as it occurred the day after his arrest.