The execution was carried out despite objections from Tokyo warning of harm to bilateral ties.
According to Xinhua news agency report, the sentence was carried out on the Japanese national, identified as Mitsunobu Akano, in the northeastern province of Liaoning.
As per reports, two countries normalised diplomatic relations in 1972. This is the first time Japanese was executed by China since the efforts to normalise relations. Despite some relief to the tensions, the countries have been having issues over territorial disputes and Japan's wartime history in China.
"Although there exist differences in the judicial system (between the two countries), it is quite regrettable from the Japanese side," Japanese Prime Minister Yukio Hatoyama was quoted as saying in Kyodo news agency before the execution.
Japan's justice minister Keiko Chiba said that the sentence was unduly harsh and expressed concern if China's actions would fan Japanese public resistance.
Japanese foreign minister Katsuya Okada, who met Chinese Ambassador Cheng Yonghua on Friday, Apr 2, also conveyed the concern about a possible Japanese backlash after China announced the execution last week.