An institute under the education ministry says Japan's output of scientific and technical literature is now ranked 4th behind China and Germany. Japan was listed as second to the US a decade ago.
The National Institute of Science and Technology Policy tallied the number of scientific papers from more than 100 countries using US databases.
It says that between 2013 and 2015, the number of papers released from universities and research institutions in Japan averaged about 64,000 per year. The figure is a 6 percent decline from the 2003 to 2005 period.
Michinari Hamaguchi of the Japan Science and Technology Agency says that without joint research with overseas peers, Japanese researchers face difficulty in getting their papers published in top-level journals.
He said many young researchers in the country are on limited-term employment and are therefore required to produce results in a short time.
He stressed the need to increase research opportunities abroad.