About an hour later, the president of the Olympic Council of Malaysia, Imran Jaafar, set off with the torch, jogging a short distance before handing it to the next runner in the relay covering 10 miles through downtown Kuala Lumpur.
"I am very excited, very honored to be the first runner. The honor is not just for myself, but also for the country," Imran said.
The relay, which started in blistering sun, ended about four hours later in blinding rain at the iconic Petronas Twin Towers after passing through the hands of 80 runners.
Criticism of China's human rights record has turned the Olympics into one of the most contentious in recent history.
Protests have dogged the torch relay during its stops in Paris, London and San Francisco, with demonstrations over China's crackdown in Tibet where it forcefully put down anti-government riots.
Witnesses said the adult couple and the boy were heckled by Chinese bystanders during the confrontation at Independence Square where the 10-mile relay began.
Scenes captured by a television cameraman showed some of the Chinese supporters striking the family members with plastic blow-up batons that they were carrying to celebrate the occasion.
Some shouted "Taiwan and Tibet belong to China" during the confrontation.
Police intervened and took the Japanese family away.
The supporters carried Chinese flags and waved banners that read: "The Torch will spread around the world," and "No one can split China."
Kuala Lumpur police chief Muhammad Sabtu Osman said the family was detained "only for documentation," and said he had no information that they were beaten by others in the crowd.
Muhammad Sabtu, the police chief, said the monk, whose nationality was not known, and the British women wearing a "Free Tibet" T-shirt were detained because they were not carrying their passports. Both were freed a few hours later, he said.
Japanese Embassy officials meanwhile were negotiating with police for the release of the family.
A group of Chinese lion dancers and drummers heralded the run through a secure corridor guarded by some 1,000 policemen and commandos.
As the runners passed through Chinatown, hundreds of schoolchildren and other Chinese supporters cheered and waved small Malaysian flags.