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Robert Gates, US defence secretary, recently fired both the US Air Force chief of staff and air force secretary after an investigation blamed the air force for the inadvertent shipment of nuclear missile nose cones to Taiwan.

According to previously undisclosed details obtained by the FT, the investigation also concluded that the air force could not account for many sensitive components previously included in its nuclear inventory.

One official said the number of missing components was more than a thousand.

The disclosure is the latest embarrassing episode for the air force, which last year had to explain how a bomber mistakenly carried six nuclear missiles across the US. The incidents have raised concerns about US nuclear safeguards as Washington presses other countries to bolster counter-proliferation measures.

In announcing the departure of the top air force officials earlier this month, Mr Gates said Admiral Kirkland Donald, the naval officer who led the investigation, concluded that both incidents had a “common origin” which was “the gradual erosion of nuclear standards and a lack of effective oversight by air force leadership”.

Mr Gates added that the Pentagon was evaluating the results of a “comprehensive inventory of all nuclear and nuclear-related materials [conducted] to re-establish positive control of these sensitive, classified components”.

Adm Donald briefed Congress on the results of his investigation on Wednesday. Bryan Whitman, Pentagon spokesman, declined to comment on the classified report.

A senior defence official said the report had “identified issues about record keeping” for sensitive nuclear missile components. But he stressed that there was no suggestion that components had ended up in the hands of countries that should not have received them.

But Daryl Kimball, executive director of the Arms Control Association in Washington, said the revelation was “very significant and extremely troubling” because it meant the US could not establish the positive control referred to by Mr Gates.

“It raises a serious question about where else these unaccounted for warhead related parts may have gone,” said Mr Kimball. “I would be surprised if the recent Taiwan incident is not the only one.”

A senior military officer said the military leadership, including Admiral Mike Mullen, the chairman of the joint chiefs, was “deeply troubled” by the findings of the so-called Donald report. He added that they would be paying close attention to recommendations for improving nuclear safeguards that Mr Gates has asked James Schlesinger, a former defence secretary, to make.