A military official told AFP news agency that the incident was reported to General Peter Pace, the chairman of the joint chiefs of staff, "and higher".
The official said the notification goes as high as George Bush, the US president.
"There are procedures in place and they kicked in and worked," the official said.
Weapons accounting
Lieutenant-Colonel Ed Thomas, a US air force spokesman, told the Military Times that the weapons were under control at all times.
Thomas said US air force policy does not permit officials to say whether nuclear warheads were involved, but said all nuclear weapons at Minot, the base where the cruise missiles were loaded, were accounted for.
"Air force standards are very exacting when it comes to munitions handling," Thomas said.
"The weapons were always in our custody and there was never a danger to the American public."
Thomas said an inquiry was launched after the incident and the crews involved in loading the missiles have been decertified from handling munitions pending the investigation's outcome.
Advanced cruise missiles can be mounted with nuclear warheads that yield between five and 150 kilotons of TNT.
The atomic bomb that was dropped in Hiroshima in August 1945 had a yield of approximately 15 kilotons.