Al-Araibi, a permanent Australian resident, was locked up in Bangkok after Bahraini officials pursued him over vandalism charges.

He spent 77 days in prison.

Australian Federal Police commissioner Reece Kershaw acknowledged a trail of bureaucratic bungles led to his detention.

Mr Kershaw said he was now working with the Department of Home Affairs to address a "lack of connectivity" between border security systems and the Interpol database.

"I have delivered a letter to Mr al-Araibi to extend AFP's apology for his unfortunate detention in Thailand," he told a Senate committee in Canberra on Monday.

"And to reassure Mr al-Araibi that the AFP is continuing to review and improve processes in consultation with other relevant agencies to ensure we respond appropriately to these matters in the future.

"The AFP is working closely with the department to resolve the overarching policy and legal questions arising from this matter."

Mr Kershaw, who has been in the job less than a month, has been briefed on the circumstances surrounding al-Araibi's detention.

"I extend my apologies for your unfortunate detention in Thailand in November 2018," he wrote to the footballer.

"Please be assured that this is in no way related to your protection status, as the AFP had no awareness you had been granted protection in Australia until after your detention.

"The AFP is continuing to review and improve processes in consultation with other relevant agencies, so that we respond appropriately to these matters in the future."

Al-Araibi was held in Bangkok after an Australian Border Force officer neglected to inform the AFP and Department of Home Affairs that al-Araibi was under protection.

This would have prevented Thailand being alerted to an Interpol red notice issued against him.

Australian Associated Press