The two leaders met in London
China has criticised Gordon Brown for taking part in talks with Tibet's exiled leader, the Dalai Lama.
The two men had a 30-minute discussion at the Archbishop of Canterbury's official residence, Lambeth Palace in London, on Friday.
Foreign ministry spokesman Qin Gang said the meeting "interfered" in China's internal affairs.
The leaders discussed human rights and ways to help China in the aftermath of the 12 May earthquake.
Mr Brown's spokesman said they also talked about "the importance of the dialogue between the Dalai Lama's representatives and the Chinese authorities".
"The PM expressed his determination to work with both sides to encourage reconciliation," he said.
But in a statement published on the Foreign Ministry's website, Mr Qin condemned the meeting and an invitation for the Dalai Lama to testify before a British parliamentary hearing on China's human rights record.
He said: "This is interference in China's internal affairs and also seriously hurts the feelings of the Chinese people."
But the Dalai Lama played down the controversy while talking to MPs on Thursday.
"For me - no differences. So long as meeting and talk - that is important. I always meet on the level we are human beings," he told the Foreign Affairs Committee.
He said his people were facing a form of "cultural genocide" at the hands of China and that Britain was not doing enough to help the Tibetan people.
But the exiled leader acknowledged there were "limitations" on what foreign governments could do.
China and Tibet have long disagreed over the status of Tibet, and China sent troops into the region to enforce a territorial claim in 1950.
The Dalai Lama and the Tibetan government-in-exile have been based in India since fleeing Tibet nine years later.
China says Tibet has officially been part of the Chinese nation since the mid-13th Century and so should continue to be ruled by Beijing.
Many Tibetans disagree, pointing out that the Himalayan region was an independent kingdom for many centuries, and that Chinese rule over Tibet has not been constant.