The statement from China's Foreign Ministry came hours after the US President met the Tibetan spiritual leader and Nobel Peace Prize laureate, who was in Washington for an 11-day Buddhist ritual.
China had already called on the US to stop Saturday's meeting, warning it could hurt relations between the two countries.
After the 45-minute private session at the White House, China said the Foreign Ministry and the Chinese Embassy had lodged objections with US representatives in Beijing and Washington.
"Such an act has grossly interfered in China's internal affairs, hurt the feelings of the Chinese people and damaged Sino-American relations," a Chinese Foreign Ministry spokesman said in the statement.We demand the US side seriously consider China's stance, immediately adopt measures to wipe out the baneful impact, stop interfering in China's internal affairs and cease to connive and support anti-China separatist forces that seek 'Tibetan independence.'"
China considers the Dalai Lama a separatist intent on ending Chinese rule over Tibet.
The Nobel laureate says he seeks only a high level of autonomy for Tibet.
The meeting came less than 10 days before US Secretary of State Hillary Clinton is due to visit the southern Chinese city of Shenzhen and meet with Chinese State Councillor Dai Bingguo, Beijing's top foreign policy official.
Vice President Joe Biden is also scheduled to visit China this summer, followed by a trip to Washington by his Chinese counterpart, Xi Jinping.
Obama last met with the Dalai Lama in February 2010, infuriating Beijing during a tension-filled year in which China and the US also feuded over online censorship and arms sales for Taiwan.
Relations were considered back on track in January when President Hu Jintao visited Washington.