The Japanese cabinet on Tuesday approved documents to ratify the accord after the upper house of parliament voted 229-0 vote in favour of it on Friday.
The pact requires industrialised countries to reduce their greenhouse gas emissions by 8% of the 1990 levels between 2008 and 2012.
But the accord still falls short of enough support needed for it to come into effect.
It needs to be ratified by nations that together account for 55% of global greenhouse gas emissions to have legal status.
All 15 European Union states ratified the pact last week. But with Japan on board too, the agreement still only has support from countries responsible for 36% of gases.
Japan's dilemma
The US alone accounted for 36.1% of greenhouse emissions in 1990. But the world's biggest polluter opted out of the pact last year, arguing that its economic interests would be threatened.
The BBC's Tokyo correspondent, Charles Scanlon, says that as hosts of the Kyoto agreement, Japan has been under intense pressure to ratify it.
For some months after the US pulled out, Japan appeared to waiver - but public opinion would not have allowed the country to walk away from the agreement.
The 55% target is expected to be reached when Russia signs up later in the year, but Japan feels strongly that the protocol will not be meaningful without the participation of the US.
US firm
Prime Minister Junichiro Koizumi on Tuesday called for the US to change its mind.
"The government of Japan will do its utmost to establish a common rule, in which all countries including the United States and the developing countries participate," he said.
Instead of cutting emissions, the Bush administration has initiated policy changes that could increase its emissions by up to 30%, the European Commission has said.
In a report just released, the US Government has acknowledged for the first time that man-made pollution is largely to blame for global warming. But it has refused to shift its position on Kyoto.
Countries supporting the protocol have been pushing for it to be ratified before the World Summit on Sustainable Development, which begins in Johannesburg in August.
The documents signed by Japan were to be submitted to United Nations Secretary-General Kofi Annan later on Tuesday.