Captured US humanitarian aid worker Kayla Mueller was repeatedly raped by the top leader of the jihadist group Islamic State, Abu Bakr al-Baghdadi, himself before her death earlier this year, counter-terrorism authorities have revealed.

The report dispelled rumours that Mueller became a willing spouse of an ISIS militant. These rumours stemmed from a smuggled letter from Mueller stating she had been treated well despite being an ISIS captive, ABC News reported.

The repeated sexual assaults was confirmed by Mueller's family who said government officials had told them that their daughter was a victim of rape by the ISIS chief himself.

"We were told Kayla was tortured, that she was the property of al-Baghdadi. We were told that in June by the government," said Carl and Marsha Mueller, parents of Kayla, who would have celebrated her 27th birthday on Friday.

Mueller was personally brought by al-Baghdadi, an Iraqi who calls himself "Caliph" of ISIS, to the home of Abu Sayyaf, a Tunisian who manages the oil and gas revenues of the Islamic extremist group.

She was repeatedly raped by al-Baghdadi who regularly visited the compound to meet with Sayyaf.

"Baghdadi was at the house of Sayyaf. He delivered Kayla Mueller, live and in person," said a counter-terrorism official familiar with the case.

ISIS claimed in early February that Mueller was killed in a coalition airstrike in Syria. Three months later, the US Army's elite hostage-rescue and counter-terrorism unit, the Delta Force, was forced to kill Abu Sayyaf in a mission to capture him when the ISIS official raised a weapon.

The new information about Mueller's one-and-a-half-year of captivity, which included torture, dispelled speculations by some officials that Mueller cooperated or became a willing spouse, which deeply hurt her family

The rumours were based on Mueller's letter released by her family, in which she wrote, about a year into her captivity, that she was "completely unharmed + healthy (put on weight in fact); I have been treated w/ the utmost respect + kindness."

The revelation on Mueller's repeated rape in the hands of the ISIS leader came from US debriefings of at least two Yazidi girls, age 16 and 18, who were also held as sex slaves in the Sayyaf compound.

Information also came from the interrogation of Sayyaf's wife, Umm Sayyaf, who was captured in the US raid.