The Department of Defense said Navy Capt. John Kirby confirmed in an interview with Fox News that the unidentified soldier was no longer in Afghanistan, but didn't say where he was taken.
"This is in accordance with our own regulations and policies to have him in a proper detention facility and to continue to be interviewed and cared for appropriately," Kirby said. "So we've moved him to an appropriate detention facility outside the country."
He said U.S. military officials have been in communication with Afghan authorities, "all the way up to President [Hamid] Karzai."
"They know we're doing this, and they know why we're doing this," Kirby said.
An Afghan official has said there is surveillance video showing the soldier returning to his outpost after the Sunday attack.
The New York Times reported the video appears to confirm U.S. reports that one gunman was involved in killing nine children, three women and four men in two villages in the Panjwai district, about 15 miles from Kandahar.
The video of the suspect was taken from a surveillance balloon used to monitor insurgent activity, the newspaper said Wednesday.
The suspect, a 38-year-old Army staff sergeant with the Third Stryker Brigade, Second Infantry Division, was shown walking back to Camp Belambi in Kandahar, where he surrendered and was taken away.
The suspect was serving his first tour in Afghanistan after being deployed to Iraq three times, U.S. military officials have said. A senior Pentagon official told CNN the man was diagnosed with a traumatic brain injury in 2010 after a vehicle in which he was riding rolled over in a crash.