"We are against foreign countries interfering in China's domestic affairs under the pretext of Tibet-related issues," Chinese Foreign Ministry spokesman Hong Lei told reporters.
"The Dalai Lama is seeking support from foreign counties to realise his political end, but he cannot succeed," Hong said.
"The Dalai Lama is a political exile who has long been engaged in anti-China separatist activities under the pretext of religion," he said.
At the high-profile event, Obama hailed "good friend" Dalai Lama, calling him as an "inspiration for freedom and dignity."
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"I want to offer a special welcome to a good friend, his Holiness the Dalai Lama, who is a powerful example of what it means to practice compassion and who inspires us to speak up for the freedom and dignity of all human beings," Obama said.
Chinese media criticised the US as a "trouble-maker" after Obama warmly acknowledged the Tibetan leader.
"Issues regarding Tibet concern China's core interests and national sentiments. Beijing has long made it clear that the Dalai Lama, who has for decades tried to separate Tibet from China, should never be hosted by leaders of other countries," official news agency Xinhua said.
The news agency warned that Obama has "dampened the hard-won positive momentum in China-US relations" by meeting the Tibetan leader.
It was the first time when Obama and the Tibetan spiritual leader have been seen together in public. Three previous encounters have been held behind closed doors.
Previous meetings of Obama with the Dalai Lama have been met with fierce Chinese protests and some of the foreign leaders had dodged their meetings with the 79-year-old monk altogether.
Beijing accuses the Dalai Lama of being a separatist seeking to split Tibet from the rest of China and tries its best to isolate the spiritual leader.
The 14th Dalai Lama, who fled Tibet in 1959 after a failed uprising against Chinese rule in his Himalayan homeland and has lived in exile in India ever since. He won the Nobel Peace Prize in 1989 for his advocacy for Tibet in the country and around the world.