Vice Foreign Minister Cui Tiankai summoned U.S. ambassador to China Jon Huntsman to lodge a "solemn representation" over Thursday's meeting at the White House, the ministry said in a statement posted on its Web site.
"The behavior of the U.S. side seriously interferes in China's internal politics and seriously hurts the national feelings of the Chinese people," the statement said, quoting spokesman Ma Zhaoxu.
The meeting was seen as another ties between Beijing and Washington, strained in recent weeks by issues from Taiwan arms sales to cyber spying allegations.
However, the language of the protest issued by the Foreign Ministry was relatively constrained, a reflection of the White House's low-key treatment of the meeting with the exiled Tibetan leader and Beijing's own desire to maintain healthy China-U.S. relations. The meeting was in the White House's Map Room, a lower-profile venue than the Oval Office.
In his statement, Ma expressed "strong dissatisfaction and resolute opposition" to the meeting.
"The Chinese side demands that the U.S. side seriously consider China's stance, immediately adopt measures to wipe out the baneful impact and stop conniving and supporting anti-China separatist forces that seek Tibet independence," said the statement, posted on the ministry's Web site.
China accuses the Dalai Lama of seeking to remove Tibet from Chinese rule and objects strongly to all contact between him and overseas leaders.
The White House said Obama told the Dalai Lama that he backs the preservation of Tibet's culture and supports human rights for its people. He also gave encouragement to the Dalai Lama's request for talks with the Chinese government.
While the meeting was long expected, the administration had taken considerable measures to limit its impact on China-U.S. relations. Obama had declined to see the Dalai Lama during his Washington stay in October because it would have come before the president's November China visit.
There was no welcome fanfare on Thursday and Obama made no public comments, issuing only a brief statement through his spokesman. The White House banned reporters and TV cameras, distributing a single photo of the two leaders.
Meetings between the Dalai Lama and U.S. presidents became standard fare under former President George H.W. Bush nearly 20 years ago. But the choreography is always delicate and closely watched because of China's sensitivities.
The meeting came at a time when U.S.-Chinese relations are particularly raw, with China warning of retaliation over the Obama administration's approval of a multibillion-dollar arms sale to Taiwan, the self-governing democratic island that Beijing claims as its own, has raised tensions.
Disputes over trade, exchange rates, and human rights have also ratcheted up tensions, although Beijing has recently seemed to indicate through the official media that it doesn't want to see a major crisis.
After the White House meeting, the Dalai Lama chided Beijing for taking a "childish" and "limited" approach to Tibet's quest for greater autonomy and said Obama had been "very much supportive" of his views on human rights and the concerns of the Tibetan people.
His envoy, Lodi Gyari, said Tibetans feeling marginalized by China would get encouragement from the session.
The 75-year-old Nobel Peace Prize winner denies China's accusations of separatism, saying he wants only for Tibetans to have a greater say over their affairs while remaining under Chinese rule. The Dalai Lama fled Tibet in 1959 and has since led a self-declared government-in-exiled in India.
China claims Tibet has been part of its territory for centuries and sent communist forces to occupy the Himalayan region in 1950. Many Tibetans say they were functionally independent for most of their history and accuse China of undermining Tibet's unique Buddhist culture and flooding the region with Chinese migrants.
Sporadic contacts between the Dalai Lama's envoys and Chinese officials were renewed last month after a break of more than a year. No breakthroughs were announced and China has made no firm indications of offering concessions to the Tibetan side.