He said that following the meeting it was up to the US to "immediately take effective steps to eradicate the malign effects" on relations.
"Obama's meeting with Dalai seriously breaks the basic rules of international relations"
Chinese foreign ministry statement
China regards the Dalai Lama as a separatist and sees any foreign official contact with him as an infringement of its sovereignty.
In an apparent attempt to avoid further inflaming tensions, White House officials kept Thursday's meeting between Obama and the Tibetan spiritual leader low-key with no media access.
The two met in the Map Room of the White House - rather than the president's Oval Office usually reserved for meeting foreign dignitaries - and only one official photograph of the meeting was released.
However, speaking to reporters outside the White House afterwards the Dalai Lama told reporters that Obama had been "supportive" during their talks which lasted around 45 minutes.
"We are fully committed to remain in the People's Republic of China," he added, but reiterated his longstanding call for "meaningful autonomy".
Beijing, he said, was taking a "childish" and "limited" approach to Tibet's quest for greater autonomy
|Only one official White House photograph of the meeting was released
After the meeting, White House officials said Obama "commended the Dalai Lama's ... commitment to nonviolence and his pursuit of dialogue with the Chinese government".
Officials said that Obama and the Dalai Lama "agreed on the importance of a positive and cooperative relationship between the United States and China".
The US president also encouraged China and the Dalai Lama's envoys to keep up efforts to resolve their differences through negotiations, despite recent talks having yielded little progress.
Obama told the Dalai Lama that he backs the preservation of Tibet's culture and supports human rights for its people, White House officials said.
Al Jazeera's Tony Birtley discusses the sensitivity of the Tibet issue in China
In a written statement issued by the foreign ministry in Beijing shortly after the meeting, China expressed disappointment that its "firm and repeated opposition" to the meeting had been ignored.
"Obama's meeting with Dalai seriously breaks the basic rules of international relations, three Sino-US Joint Communiques and China-US Joint Statement," it said.
"This meeting also breaks the promise of the One-China policy and the US position that it does not support Tibetan Independence which it has reiterated many times."
Later, summoning US ambassador Jon Huntsman to protest over the meeting, Cui Tiankui, China's vice foreign minister "lodged solemn representations" over the issue, China's official Xinhua news agency said.
In recent weeks China had repeatedly urged the White House not to go ahead with the meeting, warning it could damage ties.
Despite commanding respect by much of the international community, the Dalai Lama is seen by Beijing as a separatist seeking to overthrow Chinese rule of Tibet.
The Dalai Lama fled his homeland in 1959 following a failed uprising against Chinese rule nine years after Chinese forces occupied the Himalayan region.
The US government has often said it accepts Tibet as part of China, but Ma Zhaoxu, a foreign ministry spokesman said on Thursday that the meeting "violated the US government's repeated acceptance that Tibet is a part of China and it does not support Tibetan independence".
|The Dalai Lama fled Tibet into exile
in 1959 [GALLO/GETTY]
The meeting between Obama and the Dalai Lama comes at a troubled time in US-China relations, which have been strained by disputes over US arms sale to Taiwan and Chinese internet censorship.
The Dalai Lama's visit could also complicate Obama's efforts to secure China's help on key issues such as imposing tougher sanctions on Iran, resolving the North Korean nuclear standoff and forging a new global accord on climate change.
Adding to tensions, Obama vowed recently to "get much tougher" with China on trade issues such as trade and the value of its currency, the yuan.
Washington has long complained that China keeps its currency undervalued, hurting the competitiveness of American products.
However, official US reaction has played down the ongoing tensions.
On the eve of the Dalai Lama's visit Robert Gibbs, a White House spokesman, insisted the United States and China - the world's largest and third-biggest economies respectively - have a "mature relationship" capable of withstanding disagreements.