Foreign Ministry spokesman Hong Lei said China had made "stern representations" to the government in Ulan Bator about the Dalai Lama, who fled Tibet in 1959 after a failed uprising against Chinese rule.
"We have always opposed any country providing a platform for the Dalai Lama to engage in activities to split China in any form," he told a daily news briefing.
"The Dalai Lama always uses the opportunity of furtive visits to publicise Tibetan independence, smear the Chinese government and play up issues related to Tibet."
The Dalai Lama, fresh from a visit to Japan, arrived in the Mongolian capital on Monday for a short lecture tour at a invitation of a Buddhist group.
Ulan Bator has restricted the Dalai Lama to one lecture on Tuesday in the city's new 4,000-seat Buyant-Ukhaa sports complex, which was built using Chinese aid.
Further lectures due to be delivered on Wednesday and Thursday will be relocated to a less controversial location, Mongolian Transportation Minister Battulga Khaltmaa told reporters following a cabinet meeting.
The Nobel Peace Prize-winning Dalai Lama denies being a separatist, saying he only seeks autonomy for his homeland through peaceful means.
Buddhist monastic life, which took hold in Mongolia in the 1500s, was nearly wiped out within 15 years of communist rule, mostly during Stalinist purges in the 1930s when an estimated 17,000 lamas were executed.
But since the country emerged from decades of Soviet dominance in 1991, the Yellow Hat sect of Buddhism -- also practised in Tibet -- is making a comeback, and the Dalai Lama is recognised as one of the country's spiritual leaders.
China has been accused by human rights groups of using its growing economic clout to pressure trading partners into refusing visits by the Dalai Lama. His plans to visit South Africa earlier this year were cancelled amid accusations that the government had refused to process his visa.
Mongolia won its political independence from China in 1912, but Beijing did not recognise its sovereignty until 1946, and many in Mongolia are concerned about Beijing's growing economic hegemony.
Mongolia's booming, mining-dependent economy is almost completely reliant on its southern neighbour, with 90 percent of its exports going to China in the first half of this year.
During a previous tour by the Dalai Lama of Mongolia in 2002, China retaliated by closing the border rail crossing for two days, leaving 500 passengers stranded and severing one of the country's few links with the outside world.
Mining companies based near the Chinese border said they were not aware of any disruptions to border transport so far.