BEIJING, China (CNN) -- The protests that have surrounded the Olympic torch relay are a "crisis" but not the biggest challenge faced by the International Olympic Committee, president Jacques Rogge said Thursday.
Jacques Rogge said the IOC had expressed "serious concerns" about Tibet.
"It is a crisis, there's no doubt about that," Rogge said at a news conference in Beijing. "But the IOC has weathered many bigger storms."
Despite the protests -- which have centered around human rights in Tibet -- the torch relay will go on, but Rogge said organizers will reconsider holding such international relays for future Olympic Games.
Rogge said the committee will consider all options regarding torch relays at a meeting in September, after the conclusion of the Summer Olympics in Beijing.
He spoke as the torch was on its way to Buenos Aires, Argentina, after making its only U.S. stop, in San Francisco. Officials there shortened and changed the torch's route to bypass thousands of demonstrators. They also canceled a waterfront closing ceremony.
The relay went fairly well in San Francisco compared with chaotic relays in London and Paris, Rogge said in a statement, but "it was not ... the joyous party that we wished it to be."
Torch relays in London, Paris, and San Francisco attracted tens of thousands of demonstrators. Many want to focus world attention on China's human rights record, its actions in Tibet and its close relationship with Sudan.
In a rare mention of human rights in China, Rogge admitted that the committee hoped "awarding the games to China would advance the social agenda of China, including human rights."
His comments were immediately dismissed by a Chinese Foreign Ministry spokeswoman, who reminded Rogge that the Olympic committee's charter clearly separates the games from politics.
But Rogge said its decision was based on "a moral engagement rather than a political one.
"And we definitely ask China to respect this moral engagement," he said.
When asked about Rogge's comments, Foreign Ministry spokeswoman Jiang Yu said China has "reiterated many times" that the IOC charter calls for politics to be left out of the event.
"We hope that the IOC officials can eliminate the disruptions and stick to the clearly stated principles in the Olympic charter," Jiang said.
Rogge also pointed out Thursday that he had expressed the IOC's "serious concerns" about Tibet. He said the IOC respects protests but that they should be non-violent.
Watch IOC confirm torch relay will go on »
"We were saddened by what we saw in London and Paris. We were sad for the athletes and torch bearers. We were sad for the children who watched their heroes and role models being booed," he said. "Athletes in many countries are in disarray and we need to reassure them."
"The Games are about generosity," Rogge said. "We have 120 days to achieve this."
On Wednesday, thousands of protesters descended on San Francisco to demonstrate.
At a brief ceremony at AT&T Park, hundreds of Chinese supporters waved Chinese, American and Olympic flags. Then runners and security forces entered a warehouse.
A short time later, a motorcycle escort left the warehouse, followed by buses and vans, which carried the Olympic flame and the runners with their torches to various locations. Thousands of protesters carried banners, chanted slogans and argued with each other.
But China's state-controlled television's coverage of the San Francisco relay showed only happy supporters, waving Chinese and American flags.
The thousands of pro-Tibetan demonstrators were never seen, and there was only a brief mention the relay route change -- but the news anchor said it was because of local security and nothing more.
China has come under international criticism because of its crackdown last month on protesters calling for democratic freedoms and self-rule in Tibet and neighboring Chinese provinces. The protests had been timed to coincide with the run-up to the Beijing Games.
On Thursday, China announced it had recently thwarted another terrorist plot targeting the games -- arresting 35 people in the predominantly Xinjiang Uighur Autonomous Region.
It is the second time in recent weeks that China has announced it has uncovered a terrorist plot targeting the games stemming from separatists operating out of Xinjiang.
Human rights groups have accused China of using anti-terrorism concerns as a cover for cracking down on Muslims in the autonomous region.
Chinese authorities have denied allegations of human rights abuses and have accused the Dalai Lama of instigating violence among his followers -- an allegation the exiled Tibetan spiritual leader rejects.
Speaking Thursday at a news conference in Japan, the Dalai Lama said he reiterated his opposition to violence to Tibetans in San Francisco following the chaos and violence surrounding the torch relay in London and Paris.
"But of course, the expression of their feelings is up to them," he said. "Nobody has the right to say 'shut up' -- it's an individual right. It's actually one cause of problem inside Tibet is because there is no freedom of speech, that is the source of the problem."
Watch Dalai Lama say he supports China »
China's foreign ministry spokeswoman dismissed the Dalai Lama's statements.
"His recent speech and activities fully shows that his peaceful and non-violent claims are all lies," Jiang said. "We have heard a lot of those now. The important thing is not to hear what he says, but that to watch what he does."
Watch China play down torch coverage »
After the Buenos Aires relay on Monday, the torch will make its way across 14 more cities in Africa and Asia before returning to Beijing on August 6 -- two days before the official start of the summer games.
A report in the South China Morning Post quoted unnamed sources Thursday saying the torch-relay route in Hong Kong "will be cut short to avoid the possibility of violent protests." The Associated Press reported that Indonesia will "significantly shorten its leg of the Olympic torch relay" as a result of anti-Chinese protests.
IOC member Kevan Gosper, who is vice chairman of the coordination commission for the Beijing Games, suggested this week that the public relations nightmare that has followed the Olympic flame may make 2008 the last year for a global torch relay.
"I'm a firm believer that we had the right template in the first place, that the torch simply should go from Olympia, Greece to the host country," he said. "I would expect that the Olympic committee will review that template."
Amid the torch controversy, debate continued about whether world leaders should attend the Olympic Games' opening ceremony.
British Prime Minister Gordon Brown has decided he will not attend the opening ceremony -- but he does plan to attend the closing ceremony, when London will be recognized as the next Olympic host. Brown never planned to attend any other part of the Beijing Olympics, his office said.
World leaders who plan to skip the opening ceremony include German Chancellor Angela Merkel, Polish Prime Minister Donald Tusk, Estonian President Toomas Hendrik Ilves and Estonian Prime Minister Andrus Ansip.
Sen. Hillary Rodham Clinton, a Democratic presidential candidate, has called on President Bush to skip the opening ceremony, too.
"It is way too far in advance for us to announce the president's schedule," White House Press Secretary Dana Perino told reporters. E-mail to a friend
CNN's John Vause in Beijing, China contributed to this report