Mattis's recommendations to the White House provide "our warfighters guidance on nominating detainees for transfer to Guantanamo detention should that person present a continuing, significant threat to the security of the US", Pentagon spokeswoman Commander Sarah Higgins said.
The US military said Ahmed Muhammed Haza al-Darbi's transfer to Saudi Arabia brought the prisoner population down by one to 40 detainees.
The remaining population at Guantanamo is now 40, but Trump has vowed to send more detainees to the prison, which is located on a United States naval base on the southeastern tip of Cuba.
Previously, the last detainees to be transferred out of the facility left during the final hours of the Obama administration.
US officials have not ruled out adding to the prisoner population again and have acknowledged trouble repatriating Islamic State fighters being held by USA -backed forces in Syria, raising the possibility that Guantanamo Bay could be seen as a viable option in the future.
Al-Darbi was captured at the airport in Baku, Azerbaijan, in June 2002 and taken to the USA base in Bagram, Afghanistan.
His lead defense counsel, Ramzi Kassem, said the transfer was the culmination of "16 long and painful years in captivity" by the U.S.at Guantanamo and in Afghanistan, with his children growing up without him and his own father dying.
"My words will not do justice to what I lived through in these years and to the men I leave behind in prison", he said.
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But the divergent United States trade delegation group is likely to have differing views on the merits of such an offer.
Al Barbi has testified to being kept in solitary confinement, strung up from a door in shackles, deprived of sleep and subjected to other forms of abuse as part of his early interrogation.
'I can not thank enough my wife and our children for their patience and their love.
Al-Derbi had pled guilty in the Guantanamo Military Commission in February of 2014.
"In some cases, those countries (where the fighters came from) have stripped them of their citizenship", Mattis said. I've never been a father.
The attack, which killed a Bulgarian crew member, happened after al Darbi was already in USA custody and was cooperating with authorities, according to court documents. Now, having complied with the terms of that agreement, al-Darbi will serve out the balance of his 13-year sentence in Saudi Arabia.
Trump's predecessor, Barack Obama, signed an executive order in 2009 ordering that the detention facility be shut down. Trump reversed that policy and has vowed to continue using the center.
"Given the history of torture, unlawful detention and complete lack of justice provided there, no new detainees should ever be transferred to Guantanamo", Daphne Eviatar, a director at Amnesty International USA, said in a statement. The attack, which killed a Bulgarian crew member, happened after al-Darbi was already in USA custody and was cooperating with authorities, according to court documents.