Zhang Qingli spoke of "smashing the Dalai Lama clique"
China has denied politicising the Olympic Games following a rebuke by the International Olympic Committee over remarks made by an official in Tibet.
The International Olympic Committee (IOC) sent a letter "regretting" remarks made during a ceremony marking the passage of the torch through Tibet.
The Communist Party boss there spoke of "smashing the separatist plot of the Dalai Lama clique".
China said it had a "solid position against politicising the Olympics".
The IOC said in its letter it "regrets that political statements were made during the closing ceremony of the Torch Relay in Tibet".
"We have written to [the Beijing Organising Committee for the Olympic Games] to remind them of the need to separate sport and politics and to ask for their support in making sure that such situations do not arise again."
The torch passed through Lhasa in Tibet last Saturday.
During his speech, Communist Party boss Zhang Qingli said: "The sky above Tibet will never change. The red five-star flag will always fly above this land.
"We can definitely smash the separatist plot of the Dalai Lama clique completely."
China's foreign ministry spokesman Liu Jianchao said he was unaware of the details of the IOC letter.
But he insisted Mr Zhang was trying to foster a "stable and harmonious environment for the Olympics".
"China's solid position is against the politicising of the Olympics," Mr Liu said.
There was a wave of violent anti-China protests in Tibet three months ago.
Although there have since been talks between Chinese officials and envoys of the Dalai Lama, the exiled Tibetan spiritual leader, Beijing still accuses him of orchestrating the violence.
He says he wants meaningful autonomy, not independence.
Some of the international legs of the torch relay suffered violent protests over Chinese rule in Tibet.