"We're attempting to determine whether the new rules apply to civil aviation, commercial air flight," State Department spokeswoman Jen Psaki said.
"In the meantime, US air carriers are being advised to take all steps they consider necessary to operate safely in the East China Sea region."
But she would not be drawn on whether US officials were advising commercial airlines to advise Chinese authorities of any flight plans which take them over the islands.
China demanded over the weekend that aircraft submit flight plans when traversing its newly-declared air defence identification zone (ADIZ) which includes the disputed islands, known as Senkaku in Tokyo and Diayou in Beijing.
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The move has triggered a storm of diplomatic protest and in a show of force two American B-52 bombers overflew the area on Monday.
In a statement, Chinese defence ministry spokesman Geng Yansheng said: "The Chinese military monitored the entire process, carried out identification in a timely manner, and ascertained the type of US aircraft."
Japanese airlines, under pressure from Tokyo, stopped following China's new rules today, after initially complying.