The figure, which marked a 2.3 percent rise from the previous fiscal year, was mainly the result of more polluting energy production following the closure of the world's biggest nuclear power plant after it was damaged in an earthquake that struck northern Japan.
"The greater use of thermal power plants due to reduced nuclear power operations significantly contributed to the increase," an environment ministry official said.
The data shows that Japan's CO2 emission rose 8.7 percent from the 1990 level.
Under the Kyoto Protocol, Japan is committed to reducing its emissions by six percent from the benchmark year in the period between 2008 and 2012. Japan relies on nuclear plants for nearly one-third of its power needs.
Leaders of the Group of Eight rich nations -- Britain, Canada, France, Germany, Italy, Japan, Russia and the United States -- called at a summit in Japan in July for global cuts in CO2 of at least 50 percent by 2050, without specifying the base year.
Negotiations are under way to draft a new environmental treaty covering the period after the Kyoto Protocol's obligations expire in 2012.