However the State Department, which said the plane had since landed safely in its original destination of Dubai, denied that the Iranian military had forced down flight FZ 4359 operated by Fly Dubai.
It said the aircraft had been re-routed due to a "bureaucratic issue... Involving the plane's flight plan" and had to land in Bandar Abbas in southern Iran.
"Contrary to press reports, no Iranian jets were scrambled in this situation," the State Department yesterday said in a statement.
Washington and Tehran have not had formal diplomatic relations for three decades, since the 1979 storming of the US embassy in Tehran and the subsequent 444-day hostage crisis.
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In recent months, the two countries have been holding face-to-face negotiations on Iran's suspect nuclear program, but ties remain tense.
Several Americans are being held by Tehran despite pleas from Washington to send them home.
"We have nothing to indicate there was more to it," Harf told CNN, adding: "We really do view this as purely a bureaucratic issue."
It was not immediately clear who was on board the Fly Dubai plane, which defense officials confirmed had been chartered by the US-led NATO International Security Assistance Force.
And it remained uncertain if it was carrying any US troops flying from the sprawling Bagram military air base just outside Kabul.
Officials confirmed however that among about 100 passengers on board, there were American citizens as well as other US government contractors of different nationalities.