The treaty was reached in this ancient Japanese capital in 1997 amid fear that the rise in global temperatures could eventually lead to droughts and the extinction of some species.
UN Secretary General Kofi Annan called climate change "one of the biggest challenges of the 21st century."
"By itself the protocol will not save humanity from the dangers of climate change. So let us celebrate but let us not be complacent," Annan told a commemoration ceremony in a videotaped message.
The United States pulled out of Kyoto in 2001 in one of President George W. Bush's first acts in office, saying the treaty would hurt the US economy.
The United States and Australia, the only other major industrial country to reject Kyoto, account together for 30 percent of the world's greenhouse gas emissions.
The Bush administration points out that developing countries such as China and India have no obligations under Kyoto, meaning that their growing economies would not face the same economic burden as the United States.
China, with economic growth close to double digits, is by some forecasts expected to exceed the United States as the world's top polluter by 2020. Developing countries will be asked to make commitments in the next phase of the Kyoto treaty, with talks due from November 28 to December 9 in Montreal.
More than 300 environmental activists marched through Kyoto under persistent rain to celebrate the start of the pact despite years of doubt, with some dressed as monkeys or penguins or wearing mock tiger ears to highlight global warming's impact on animals.
German Environment Minister Juergen Trittin, in a videotaped address to ceremonies here that ushered in Kyoto as a UN treaty, scolded the United States and urged a switch to cleaner energy sources.
He pointed to scientific advice to prevent Earth from warming more than 2.0 C (3.6 F) above pre-industrial levels.
Earth's surface has already warmed by 0.7 C (1.25 F) since 1900 as a result of burning oil, gas and coal, and this may already be affecting the climate system, scientists say. "The window of opportunity in which compliance is still possible will close in 10 to 20 years," Trittin said.
"We cannot afford to be inactive. We have to reduce global emissions by around 50 percent by the middle of this century," Trittin, a member of the Greens environmentalist party, said.
The United States and Australia were on the defensive as Kyoto took effect, insisting that they rejected the treaty for legitimate reasons and were committed to reducing pollution.
"Until such times as the major polluters of the world, including the United States and China, are made part of the Kyoto regime it is next to useless and indeed harmful for a country such as Australia to sign up for the Kyoto Protocol," Prime Minister John Howard told parliament.
White House press secretary Scott McClellan said the Bush administration had "made an unprecedented commitment to reduce the growth of greenhouse gas emissions in a way that continues to grow our economy."
"There's a lot that we are still learning about the science of climate change, but this administration is working to advance that science and to learn more about climate change itself and its effect on the world," he said. But the Bush administration's view on global warming is disputed by most of the scientific community which believes pollution can in time shrink polar ice gaps and melt alpine glaciers.
Kenyan environmentalist Wangari Maathai, the 2004 Nobel Peace laureate, told the ceremony here that many in the developing world set on "catching up with the highly industrialised world are not willing to be persuaded to slow down." "Many of us have become used to our lifestyle and are not easily persuaded to consume less and reduce greenhouse gases," she said.
"Today marks the end of a long process for the survival of all species on the planet, including our own," she said.