It said that temperatures were particularly high in eastern Russia and northern Europe.
"Reasons behind the high temperatures are considered to be the impact of global warming due to an increase in carbon dioxide, along with El Nino and the cyclical natural movement in temperatures," an agency statement said.
The study came a week after a UN report blamed human activities for global warming and predicted a rise in typhoons, droughts and other natural disasters.
The report of the Intergovernmental Panel on Climate Change warned that temperatures could rise by between 1.1 and 6.4 degrees Celsius by 2100.
Japan, the host of the landmark Kyoto Protocol meant to fight global warming, has experienced an unusually warm winter with little snow.
However, the Meteorological Agency said Japan's temperature in January was only the fourth highest on record, at 1.44 degrees above normal. The record was in January 1989 when temperatures in Japan were 2.09 degrees higher.powered by performancing firefox