Police work at the scene where a car crashed through a barrier near the Israeli embassy in Tokyo on November 16, 2023. AFP
Video footage appeared to show that the Daihatsu car was driven through a temporary barrier and into a fence at an intersection around 100 metres (109 yards) from the embassy.
Media also reported that one police officer was lightly injured in the incident late morning in the Japanese capital.
The man arrested on the spot is a member of a right-wing group and in his 50s, the reports said.
Right-wing groups in Japan are generally not known for being critical of Israel or anti-Semitic.
A fire department spokesperson said only that they received "an emergency call (for an ambulance)... at 11.57 (am)".
Police declined to comment and the Israeli embassy could not be reached.
Countries around the world have stepped up security around Israeli diplomatic missions since the start of the Israeli war on Gaza last month.
On October 21 four people were arrested after a pipe bomb exploded near the Israeli embassy in Cyprus, causing little damage and no injuries, police said.
On October 14, an employee of the Israeli embassy in China was attacked in Beijing. A foreign suspect was arrested and authorities have not said anything about the case since.
There has also been a sharp rise in anti-Semitic as well as Islamophobic incidents around the world.