Rogge told the heads of the 205 national committees to reassure their respective athletes that the Beijing Games in August would be a success.
"Tell them that whatever they have seen and heard, the Games will be very well-organised," he said.
"Tell them that we will rebound from this current crisis."
Rogge, a former Olympic yachtsman, said the Olympics will rebound as it had done in the past, referring to the 1972 Munich Games which he said was the biggest crisis in the event's history.
But his use of the word ''crisis'' came as a surprise.
Anti-China protests have snowballed along the torch's path through London, Paris and San Francisco, and pro-Tibet demonstrations are expected in the flame's only stop in Latin America.
The Olympic flame arrived in Argentina greeted by heavy police presence following concerns over anti-China protests and a warning of a Buenos Aires "surprise".
Argentinian authorities on Thursday deployed thousands of police and volunteers to ensure security.
Modern tradition of torch relay began in 1936 at Berlin Olympics
This year's is the longest ever, travelling 137,000km
The torch will visit 19 nations over 130 days
First destination is Kazakhstan
On the final leg, it will travel throughout China, including Tibet and the summit of Mount Everest
Click here to go to the official torch relay site
(Al Jazeera is not responsible for the content of external websites)
Francisco Irarrazabal, a government sports official, said the torch and a Chinese delegation arrived without incident but the flame was kept in a "safety lantern" and remained out of public view.
Indonesia has agreed to significantly shorten its leg of the torch relay, scheduled for April 22, following concerns by Chinese officials of attracting pro-Tibet protesters if the original route is maintained.
Kevin Rudd, the Australian prime minister, said the torch will pass through Canberra on April 24 but Chinese security agents escorting it will have to travel by bus during the relay.
"The total security needs of the Olympic torch during its visit to Australia will be provided by the Australian security authorities," he said in Beijing after meeting the Chinese premier, Wen Jiabao, in Beijing.
On Wednesday Rogge called on China to respect the commitment to improve human rights it made during the bid to host the Olympics.
But China responded by urging the IOC to keep "irrelevant political factors" away from the Games.
"I believe IOC officials support the Beijing Olympics and adherence to the Olympic charter of not bringing in any irrelevant political factors," Jiang Yu, a foreign ministry spokeswoman, said.
"I hope IOC officials continue to adhere to principles of the Olympic charter."
World leaders are facing pressure from human rights groups to boycott the opening ceremony of the Olympics in the Chinese capital.
Gordon Brown, the British prime minister, and Angela Merkel, the German chancellor, have already said they will not attend the August 8 ceremony and Nicolas Sarkozy, the French president, is considering staying away.
Now the United Nations has said that Ban Ki-moon, the secretary-general, will not be able to attend either.
Marie Okabe, a spokeswoman, said China was informed "some months ago" about a scheduling conflict but declined to give any details.
She added that Ban was planning "a substantive visit to China" at a later date.
George Bush, the US president, has come under pressure at home to skip the Beijing opening ceremony and the European Parliament has urged leaders of the 27 nations in the bloc to boycott the opening bash as well unless China starts talks with the Dalai Lama over the situation in Tibet.