3.8% reduction of total GHG emissions in 2020 compared to 2005 levels.
"Just before COP19, at the meeting of the Global Warming Prevention Headquarters in November 2013, Japan’s GHG emissions reduction and absorption target to 2020 was announced as being that Japan will reduce its emissions by 3.8% compared to the 2005 level based on the order from the Prime Minister."
"On November 29, the Government of Japan submitted the target, replacing the 25% reduction target, which had been submitted to the UNFCCC, in accordance with the Copenhagen Accord. This target is a target at this point, which has not yet taken into account the emission reduction effect resulting from nuclear power, given that the energy policy and energy mix, including the utilization of nuclear power, are still under consideration."
Source: http://unfccc.int/files/national_reports/annex_i_natcom/submitted_natcom/application/pdf/nc6_jpn_resubmission.pdf