November core consumer prices were off 0.1 percent year-on-year, Kyodo News reported.
The numbers are the first since the new government of Prime Minister Shinzo Abe took over this week with a mandate to kick start the recession-threatened economy, already burdened by deflation or falling prices, and declining exports. The devastating earthquake in March of last year also has hurt the economy.
The November output decline was the first in two months, the government said.
The central bank has been urged to aggressively ease monetary policies and raise the inflation target to prevent the world's third largest economy from slipping into another recession.
"We have to absolutely prevent the bottom from falling out of the economy," Chief Cabinet Secretary Yoshihide Suga quoted Abe as saying during an extraordinary Cabinet meeting.
"This is a clear indication that deflation is really ingrained in Japanese economy and it is inevitable that the central bank will have to do something to tackle it," Martin Schulz of Fujitsu Research Institute told the BBC.