The nine-page document was published by Egyptian newspaper al-Badil in April - before the outlet was banned by Cairo - accusing Saudi Crown Prince Mohammed bin Salman and Abu Dhabi's Mohammed bin Zayed of providing aid to the two extremists.
The communique - sent to Qatar's foreign minister on October 26, 2016 - outlines the minutes of communications between Qatar's ambassador to Washington and the US Treasury Undersecretary for Terrorism and Financial Intelligence.
The New Arab could not independently verify the authenticity of the documents.
"The Under Secretary for Terrorism and Financial Intelligence reported that the information available to them indicated that Prince Mohammad bin Salman has been in constant communication with the figures listed in the report," the leaked notes read.
"The prince has managed, according to the Under Secretary, to assemble out of some groups loyal to al-Qaeda in the Arabian Peninsula [AQAP] a force against the Houthis.
|The New Arab could not independently verify the authenticity
of the documents [al-Badil]
"The Under Secretary expressed his concern that Prince Mohammad bin Salman was working with al-Qaeda and extremist Salafi groups in the region without prior coordination with us," they added.
The report said bin Salman has been communicating with al-Hasan Ali Ali Abkar and Abdallah Faysal Sadiq al-Ahdal, who the US imposed sanctions on in 2016 for setting up a "front charity" to support AQAP.
The US considers the Yemen-based AQAP to be the group's most dangerous branch and has conducted a long-running drone war against its leaders.
AQAP has taken advantage of war between the Saudi-backed Yemen government and the Houthi rebels to expand its presence in several areas of eastern and southern Yemen.
"Since at least autumn 2012, Abkar was a AQAP fighter and travelled with a group of other sheikhs to Saudi Arabia and the United Arab Emirates to meet with Saudi princes and the Crown Prince of Abu Dhabi, Mohammed bin Zayed," the Qatari documents alleged.
They also revealed that Abkar received $1.6 million in 2015 through Saudi intelligence chief Khalid bin Ali al-Humaidan to provide military equipment to AQAP and the Islamic State group.
In December 2016, the two Yemeni men and the Rahmah Charitable Organisation were added to the US Treasury's list of specially designated nationals and entities that support or engage in terrorism.
The department said in a statement at the time that Abkar had provided monetary and military support to AQAP since 2014 and that he was a commander responsible for the Marib and al-Jawf areas.
It added that Ahdal had supported AQAP since 2009 by supplying funds and managing foreign fighters and that he had been a senior tribal leader in the Hadramawt region.
Bin Salman, the chief architect of Saudi Arabia's devastating two-year war in Yemen, was appointed as heir to the throne last month by royal decree, removing the country’s counter-terrorism czar from the royal line of succession.
The 31-year-old is also thought to be behind Riyadh's recent attempted isolation of Qatar.
On June 5, Saudi Arabia, the UAE, Bahrain and Egypt abruptly severed diplomatic ties with Qatar and accused Doha of funding extremist groups.
Qatar has categorically denied the charges.
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