A brief report by the Xinhua news agency broke China's media silence on the case, which began days before China and the United States were due to hold high-level talks in Beijing.
A senior US official confirmed that Chen was out of the embassy, where he had gone after fleeing from house arrest in his home province of Shandong on April 21.
"Chen Guangcheng has arrived at a medical facility in Beijing where he will receive medical treatment and be reunited with his family," said the official who requested anonymity.
China's Foreign Ministry said it was extremely unhappy the embassy had taken Chen in.
"It must be pointed out that the United States Embassy took the Chinese citizen Chen Guangcheng into the embassy in an irregular manner, and China expresses its strong dissatisfaction over this," ministry spokesman Liu Weimin said in a statement carried by Xinhua.
"The US method was interference in Chinese domestic affairs, and this is totally unacceptable to China.
China demands that the United States apologise over this, thoroughly investigate this incident, punish those who are responsible, and give assurances that such incidents will not recur."
US Secretary of State Hillary Clinton arrived in China on Wednesday for the top-level talks that risk being upstaged by the Chen case.