US special operations forces have killed an Islamic State commander through a dramatic and secretive raid into Syria and have taken a woman prisoner, the first US-held detainee of the war against Isis and a move that places immediate stress on one of Barack Obama’s signature wartime policies.

Ashton Carter, the US defense secretary, confirmed on Saturday that Obama ordered the elite troops to raid a location in eastern Syria and “capture” an Isis figure, Abu Sayyaf. Unusually, Carter said the raid also targeted the man’s wife, identified as Umm Sayyaf.

Abu Sayyaf was killed in the raid, Carter said. Umm Sayyaf was taken prisoner – a rarity for the Obama administration, whose reluctance to add to the complexities of US wartime detentions has often led it to kill battlefield targets instead of capturing them.

A White House statement indicated the Iraqi government “contributed” to the operation, involvement that could signal Umm Sayyaf’s ultimate dispensation.

Bernadette Meehan, the National Security Council spokeswoman, said Umm Sayyaf was “in military detention in Iraq”. US officials did not immediately respond to requests for elaboration about her conditions and what they intend to do with her.

But the administration was portraying the overall operation as a success.

“The operation represents another significant blow to Isis, and it is a reminder that the United States will never waver in denying safe haven to terrorists who threaten our citizens, and those of our friends and allies,” Carter said in a statement.

Meehan said in a separate statement that the operation also freed a young Yazidi woman whom Abu Sayyaf and Umm Sayyaf kept as “a slave”. Isis members have committed human trafficking and slavery, particularly against the Yazidi minority whose persecution on a mountaintop in Iraq last year sparked Obama to begin airstrikes on Isis.
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Although the raid was described to reporters as a capture mission, Meehan indicated that the US was unsure what it would do now it has Umm Sayyaf in custody.

“We are working to determine an ultimate disposition for the detainee that best supports the national security of the United States and of our allies and partners, consistent with domestic and international law. We will follow our usual practice with respect to giving the ICRC notification and access to the detainee,” Meehan said, referring to the International Committee of the Red Cross.

A Pentagon spokesman said she did not know if Umm Sayyaf was being interrogated or would soon be. Nor did she know if Umm Sayyaf would be taken to Guantánamo Bay.

The 3,000 US military forces on the ground in Iraq, formally on an advisory mission, are not known to operate any detention facilities – an allergy in Iraq after the infamous Abu Ghraib torture scandal of the last decade’s US occupation. Transferring Umm Sayyaf to Iraqi prisons, a possible outcome of the raid, is also complicated by US and international injunctions against turning detainees over to abusive prison conditions.

Human Rights Watch has documented extensive abuse, to include rape, in Iraqi government jails.

In a 2014 report, the monitor organization determined that “security forces of the interior and defense ministries, and forces that operate unofficial detention facilities, tortured women in their custody”.

US warplanes bomb Isis positions in Syria daily. Raids by ground forces have been rare. A publicly acknowledged exception was a summer 2014 attempt to free western hostages from Isis captivity. By the time US forces arrived at their target location, the hostages had been moved. Some, including journalist James Foley, would later be beheaded by Isis.