The UK Foreign Office has formally apologised to the academic Matthew Hedges for its handling of his arrest and subsequent torture by the United Arab Emirates.

The apology was recommended by the parliamentary ombudsman after Hedges filed a complaint.

In a letter signed by the Foreign Office’s top official, the permanent undersecretary Sir Philip Barton, it acknowledged the profound impact the arrest had on Hedges and the injustice he faced. Hedges was given £1,500 in nominal compensation, as recommended.

Barton said the Foreign Office’s handling of Hedges’s arrest was not in line with its guidelines on how to look for signs of torture, but added that in practice it led to the same outcome as if the guidelines had been followed.

He said the Foreign Office urgently sought with UAE officials further consular visits with Hedges even though the case was not formally referred to the department’s human rights adviser as the guidelines suggest.

Hedges welcomed the apology but said it was baffling that the British government still wanted such close relations with a Gulf partner that had mistreated British people.

In a report published last month, the ombudsman found that at every meeting with a Foreign Office consular official, the UAE guards allegedly responsible for Hedges’ torture were present, making it impossible to be open about his mistreatment.

He was arrested in May 2018 at Dubai airport on suspicion of being a British spy and then released after a media campaign led to his pardon in November 2018. He had been sentenced to life imprisonment.

In the recommended letter of apology, Barton said he recognised “the profound impact of your detention in UAE on you and the injustice you have faced”.

He added: “On behalf of the Foreign, Commonwealth and Development Office [FCDO], I acknowledge, and apologise for, the failing identified by the ombudsman, specifically I recognise that we did not fully follow our guidance on torture and mistreatment and that this failure has left you uncertain as to whether more could have been done on your behalf.”