The official largely confirmed a Wall Street Journal report which said the training has been going on for at least a year, amid China's rising verbal threats against the island ally of the United States.
Beijing opposes self-ruled Taiwan -- which it views as its own territory to be seized one day, by force if necessary -- having any official diplomatic exchanges and has aggressively tried to dissuade politicians from visiting in recent years.
China reacted angrily to the report Friday, with the foreign ministry warning that the US should recognise the "high sensitivity" of the Taiwan situation and "serious harm" of its actions.
"The US should ... stop arms sales to Taiwan and US-Taiwan military ties, so as not to seriously damage China-US relations and peace and stability in the Taiwan Strait," foreign ministry spokesman Zhao Lijian said at a briefing.
"China will take all necessary measures to safeguard its sovereignty and territorial integrity."
Taiwan's defense ministry declined to comment on the report, but Pentagon spokesman John Supple said that generally speaking, US support for Taiwan's military is gauged on its defense needs.
"Our support for and defense relationship with Taiwan remains aligned against the current threat posed by the People's Republic of China," Supple said in a statement.
Taiwan media reported last November, citing Taiwan's Naval Command, that US troops had arrived there to train the island's marines and special forces in small-boat and amphibious operations.
But those reports were subsequently denied by US and Taiwanese officials, who emphasized the two sides are only involved in bilateral military exchanges and cooperation.
The US supplies weapons to Taiwan, including missiles for defense and fighter jets, in a bid to counter Beijing, which has threatened to forcibly retake control of the island and unify it with China.
Washington also maintains an ambiguous commitment to defend Taiwan.
A video released last year and featured in Taiwan media showed US troops taking part in an exercise on the island dubbed "Balance Tamper."
Chinese forces have stepped up their activities toward Taiwan in the past year, conducting sea assault exercises and flying large sorties of bombers and fighters close to Taiwan airspace.
Taiwan's defense minister said Wednesday that military tensions between the island and China are at their highest in four decades, after around 150 Chinese warplanes -- a record number -- made incursions into its air defense zone in recent days.
He warned that even "slight carelessness" or "miscalculation" could spark a crisis, and that Beijing would be in a position to launch a full-scale invasion in four years.