The test missile had been launched from Vandenberg Air Force Base at about 3 a.m. and was destroyed just five minutes later because of safety concerns.
Air Force Col. Matthew Carroll said controllers detected what's being described as a "flight anomaly."
"Established parameters were exceeded and controllers sent destruct commands," Carroll said in a statement. "When terminated, the vehicle was in the broad ocean area northeast of Roi-Namur." That's an area near the Kwajalein Atoll in the Marshall Islands, the Air Force said.
There were no details on what went wrong. The Air Force said there will be an investigation.
It's the second Minuteman 3 test problem in five weeks at Vandenberg Air Force Base, located on the coast about 130 miles northwest of Los Angeles.
The Associated Press contributed to this report.