Monday's meeting was the first time between a Canadian prime minister and Tibet's exiled spiritual leader in federal government offices. The red-carpet treatment that Ottawa laid on was just the latest in a string of warm Western welcomes for the Dalai Lama.
Chinese Foreign Ministry spokesman Liu Jianchao called the meeting a "gross interference" in China's internal affairs.
"We express strong dissatisfaction," he told a news conference Tuesday. "We hope they can reflect on and correct the erroneous actions."
The Dalai Lama is lauded in much of the world as a figure of moral authority, but Beijing demonizes the 1989 Nobel Peace Prize laureate and claims he seeks to destroy China's sovereignty by pushing for Tibet's independence.
China has ruled with a heavy hand since its communist-led forces invaded in 1951. The Dalai Lama, who is immensely popular in Tibet, says he wants autonomy for the Himalayan region, not independence.
Harper followed in the footsteps of U.S. President George W. Bush and German Chancellor Angela Merkel in choosing to meet with the Dalai Lama in public and at official venues, giving the impression he has their political support.
The Dalai Lama has lived with followers in exile in northern India since fleeing Chinese soldiers in Tibet in 1959, and said Monday that suppression of religion, language and culture is getting worse in Tibet.
The Dalai Lama was granted honorary Canadian citizenship in 2006.