Japan’s F-4 Phantom jet struck a Chinese fighter jet near the border of Hainans and Guangdong provinces, according to a local government statement.
China has expressed outrage over the incident, saying the plane was not a warplane and was carrying out an anti-submarine mission.
The incident occurred on the border between the two countries, the statement said.
It was not immediately clear how many casualties were involved in the incident.
The plane had been carrying out a surveillance mission over Hainanz, the Chinese province of Heilongjiang, to check out the weather conditions there, the government statement said, without giving further details.
The plane was flying around 2,000 kilometers (1,600 miles) from the Chinese border, the spokesman for the Hainane military said.
The attack is a major setback for the Japanese fighter jets, which have struggled to regain ground lost to China in recent years as its military advances in the South China Sea.
China says the F-5 jets are carrying out anti-aircraft and anti-ship patrols in the area.
The aircraft’s role is to patrol the sea, not conduct combat missions, the country’s state media has said.
Japanese Prime Minister Shinzo Abe has called on China to make an apology to Japan and stop its provocative behavior in the disputed South China Seas, a stance that Beijing regards as a threat to its sovereignty.
Chinese foreign ministry spokeswoman Hua Chunying told reporters the F4 was returning from an air show over Haina when it was struck by a Chinese air defense system.
She said the incident had happened in the “totally uncontrolled zone” where the F5s are operating.
China’s foreign ministry has not commented.