The U.S. military misplaced hundreds of sensitive nuclear missile components, but they weren't lost -- they just weren't where they were supposed to be, a Navy source told FOX News on Thursday.

The Navy source close to Defense Secretary Robert Gates said that Gates ordered Adm. Kirkland Donald to investigate the nation's nuclear security in the wake of the military's accidental shipment of nuclear cones to Taiwan. The investigation called on the Air Force, Navy and Defense Logistics Agency to inventory all of their nuclear components.

Gates said the Pentagon would take inventory of every piece of nuclear weapon-related parts "to re-establish positive control of these sensitive, classified components," according to Thursday's Financial Times.

The investigation discovered "the gradual erosion of nuclear standards and a lack of effective oversight by air force leadership," Gates said.

The Financial Times reported that the U.S. Air Force did not know the whereabouts of the nuclear missile components or other nuclear parts. One official said the number of missing components was more than 1,000.

The Defense Logistics agency also could not account for a variety of nuclear components, as paperwork was not done from an inventory perspective. However, the Navy source told FOX News the components were not "lost," but were found in other secure classified locations.

Navy officials came back with 100 percent compliance, accounting for all of the service's nuclear components, the source said.

A senior defense official told the newspaper that the investigation did not mean that missing nuclear parts were in the hands of countries that should not have taken receipt of them.

"[It] identified issues about record keeping," he said.

Gordon Johndroe, National Security Council spokesman, declined to comment on the disclosure about the unaccounted components. But, Johndroe said, "The White House has confidence that Secretary Gates through his actions with the Air Force is addressing all of these issues."

Both the Air Force chief of staff and secretary, the military and civilian chiefs of the service, were asked to resign recently after the investigation's findings were revealed.

Click here to continue reading the report at FT.com

FOX News' Jennifer Griffin and Mike Emanuel contributed to this report.