Trump originally misspelled "unprecedented," but later deleted the tweet and reposted.
The drone was launched by the USNS Bowditch, a civilian crewed oceanographic ship that is operated by the Military Sealift Command, off the coast of the Philippines. These types of drones, called gliders, typically collect unclassified data, such as water temperatures and salinity levels.
According to Cook, the drone is not armed and is used for gathering weather and temperature data. The incident occurred Thursday.
The Bowditch was about to recover the glider when a Chinese Dalang III class Chinese warship approached within 500 yards of the Bowditch, launched a small vessel and snatched the drone out of the water, the Pentagon said.
The boat brought the device back to the Chinese warship, which then headed away.
The Bowditch contacted the Chinese vessel by radio and demanded the return of the glider. The Chinese ship acknowledged the radio transmission but ignored the request to return it, the Pentagon said.
The U.S. government has issued a démarche, or diplomatic protest, over the incident, demanding its return.
The incident comes at a sensitive time in U.S.-China relations. President-elect Donald Trump has been critical of the Chinese, saying they have gotten the better of trade deals between the two nations.
The South China Sea is a region where the Chinese have attempted to extend their influence and military presence. The U.S. has insisted on its right to transit through the region in international waters.