The Australian Federal Police (AFP) boss has personally apologised to refugee footballer Hakeem al-Araibi over his detention in a Thai prison for months.

Key points: Hakeem al-Araibi was arrested when he travelled to Thailand for his honeymoon and spent 77 days in prison

Hakeem al-Araibi was arrested when he travelled to Thailand for his honeymoon and spent 77 days in prison Prime Minister Scott Morrison personally intervened in the case, urging his Thai counterpart to release Mr al-Araibi from detention

Prime Minister Scott Morrison personally intervened in the case, urging his Thai counterpart to release Mr al-Araibi from detention Commissioner Kershaw described the bureaucratic failure as a "lack of connectivity" between government agencies and Interpol

Commissioner Reece Kershaw, who assumed the AFP's top job earlier this month, told Senate Estimates bureaucratic mistakes led to the permanent Australian resident being locked up.

Mr al-Araibi was arrested by Thai authorities when he arrived in Bangkok for his honeymoon in November 2018, because Bahrain had issued an Interpol red notice against him for vandalism charges.

Mr al-Araibi has long maintained Bahrain's allegations were politically motivated.

Commissioner Kershaw said he felt the need to write directly to the footballer to say sorry, having reviewed the case after he took over the leadership of the AFP.

"I have delivered a letter to Mr al-Araibi to extend AFP's apology for his unfortunate detention in Thailand," Commissioner Kershaw said.

"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.

"As an accountable organisation to the community, I felt it was right to do," he said.

Mr al-Araibi spent 77 days in detention and was only released when the case to extradite him to Bahrain was dropped.

Hakeem al-Araibi spent months in a Thai jail because of mistakes made in Canberra. ( ABC News: Elena de Bruijne )

His arrest and detention attracted widespread criticism in Australia.

Prime Minister Scott Morrison personally intervened in the case, urging his Thai counterpart to release Mr al-Araibi from detention.

Commissioner Kershaw told the Senate AFP officials had been unaware he had been granted protection in Australia until after he was detained in Thailand.

Had Border Force informed the AFP and Department of Home Affairs about his protection status, Thailand would not have been alerted to the red notice issued against him.

Commissioner Kershaw described the bureaucratic failure as a "lack of connectivity" between government agencies and Interpol.