"China steals United States Navy research drone in international waters - rips it out of water and takes it to China in unpresidented act," Trump said on Twitter, later correcting the misspelling to "unprecedented."
The drone was seized by the Chinese navy on Thursday off the coast of the Philippines.
"It is understood that China and the United States are using military channels to appropriately handle this issue," China's Foreign Ministry said in a statement, according to Reuters.
Pentagon spokesman Peter Cook on Friday called on China to return the drone, Politico reported.
"It is ours, and it is clearly marked as ours and we would like it back. And we would like this not to happen again," Pentagon spokesman Jeff Davis said.
In the weeks since he was elected, Trump has added controversy to the U.S. relationship with China, taking a phone call from the president of Taiwan and then suggesting that the U.S. might no longer recognize the longstanding "one China" policy.
China has moved to claim the South China Sea as its own territory, sparking pushback from the U.S. and others in the international community.