The officials, speaking on condition of anonymity, cited unspecified intelligence gleaned about the case. A U.S. intelligence official said it was unclear whether Mueller was coerced, sold or forced into the pairing.
Intelligence suggests Mueller may have been given to an ISIS fighter as a sort of bride, one U.S. government official said.
The National Security Council said it was breaking with protocol to make a statement about an American hostage.
"Reports that have been published by certain news outlets regarding Kayla's time in (ISIS) captivity are speculative and unproven at this time," spokeswoman Bernadette Meehan said. "The U.S. government continues to analyze any information regarding Kayla's captivity but has not corroborated any of the multiple theories regarding the conditions throughout the duration of her captivity."
Mueller's parents announced Tuesday that it had received confirmation that their daughter, who was captured in northern Syria in 2013, had died.
ISIS sent the family a private message over the weekend with information about her death, Meehan said Tuesday.
The message included photos. One picture showed her wrapped in a burial shroud, but there was enough showing for the family and forensics examiners to identify her, a U.S. official briefed on the matter told CNN.
The information did not confirm how Mueller died, a law enforcement source familiar with the case said on condition of anonymity.
On Friday, ISIS said that Mueller, 26, of Arizona, had been killed in a building hit during a Jordanian airstrike on Raqqa, the militants' de facto capital in Syria. At the time, ISIS offered no proof to back up its claim, other than an image of a building in rubble.
The photos in the private weekend message showed bruises on the face, The New York Times
reported, but it was unclear whether her injuries were consistent with being killed in the rubble of a flattened building, as ISIS claimed.
Rescue attempts failed
Mueller made it her life's work to help others. She was a 2009 graduate of Northern Arizona University and worked with humanitarian groups in northern India, Israel and Palestinian territories, a family spokeswoman said.
"She had a quiet, calming presence. She was a free spirit, always standing up for those who were suffering and wanting to be their voice. ... Kayla's calling was to help those who were suffering, whether in her home in Prescott, or on the other side of the world," her aunts, Lori Lyon and Terri Crippes, said Tuesday.
In August 2013, Mueller fell into the hands of hostage-takers in Aleppo, Syria, her family said, after leaving a Doctors Without Borders hospital she was visiting.
Her family said ISIS contacted them in May with proof that she was alive. The militants eventually said they would kill her if the family didn't pay nearly $7 million by August 13, according to a source close to the family.
A number of rescue and negotiation attempts to free Mueller failed, officials said.
Rep. Paul Gosar, R-Arizona, told CNN's Jake Tapper that he and his staffers tried to facilitate Mueller's release on several occasions. Negotiations between the family and ISIS at one point, he said, included discussion about whether Mueller could be swapped for Dr. Aafia Siddiqui, a prisoner being held in Texas who was convicted for conspiring with the enemy.
Source: Family asked if deal would be made
The Mueller family reached out to the White House last summer when ISIS issued a deadline to execute Kayla and asked if the government would be willing to trade Siddiqui, known as "Lady Al Qaeda," in exchange for Mueller, a spokeswoman for the family said. ISIS has repeatedly made public calls for Siddiqui's release.
"The family was doing everything it could to bring their daughter home," the spokeswoman said. It asked the White House if it could have Siddiqui's sentence commuted. The White House responded, but the spokeswoman would not say what the answer was.
The request to the White House was first reported by the Daily Beast.
Mueller was still alive after the ISIS-imposed deadline to execute her, the spokeswoman said, although she didn't specify how that was known.
Mueller's boyfriend, who was captured with her but later released, posed as her husband and risked his life trying to rescue her from a terrorist training camp in Syria, the spokeswoman said. He still talks with the family.
Orouba Barakat, a friend of Mueller, said she received a short audio clip made by Mueller after she was kidnapped.
"She begged for help. 'Please try to help me, get me out (of) here. I'm so sick, I'm dying,' " she said, recalling the audio.
Barakat, a Syrian journalist who met Mueller while in Turkey, said she heard the 10- to 15-second recording about three months after Mueller was abducted. She tried contacting Mueller by Skype and by email, but never heard back from the hostage.
President Obama: "We devoted enormous resources"
U.S. President Barack Obama said Tuesday that the government had worked to free Mueller and other hostages.
"We devoted enormous resources, always devote enormous resources to freeing captives or hostages anywhere in the world. And I deployed an entire operation -- at significant risk -- to rescue not only her but the other individuals who had been held, and probably missed them by a day or two, precisely because we had that commitment," Obama said in an interview with BuzzFeed News.
Confirmation of Mueller's death drew condolences and tributes from across the country and around the world. In Jordan, where seething leaders have vowed revenge after ISIS burned a captive Jordanian pilot to death
, government spokesman Mohammed Al-Momani expressed "grief and anger" over Mueller's death.
Arizona Gov. Doug Ducey said
he had ordered flags at state government buildings to fly at half-staff until sundown Wednesday in her honor.