The Australian Federal Police was not aware footballer Hakeem al-Araibi was a refugee until after his detention in Thailand.
The 25-year-old was on his honeymoon in November when Bahrain requested an Interpol red notice against his name and he was detained upon landing in Bangkok.
Interpol did not know Mr al-Araibi was a refugee, and would not have issued the notice had they known.
"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 a Senate estimates hearing on Monday.
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 told senators in Canberra.
The visa status was not known until after his detention in Thailand.
"Neither the AFP nor the Australian Interpol NCP can access this information; we rely on notifications from the Home Affairs department," Mr Colvin said.
"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The AFP then referred his visa status to Interpol's legal affairs department, and Mr al-Araibi's red notice was rescinded on December 1.
Mr Colvin said the AFP held fire on correcting the record over the handling of Mr al-Araibi's case so as not to prejudice his case.
"This was a decision made in what we thought was the best interests of Mr al-Araibi," he said.
"While it did not sit well with my members to be subject to wrongful speculation about the AFP's involvement in this matter, the priority was to ensure a safe return to Australia for Mr al-Araibi."
Mr al-Araibi was freed earlier this month after spending two months in detention.
Home Affairs officials are conducting a review into Mr al-Araibi's case to reduce the risk of similar incidents in the future.
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