Public broadcaster NHK said the five or six Molotov cocktail-like objects hit a riot police vehicle, but the fire was soon extinguished and no one was injured. Police were unable to immediately confirm the reports to AFP.
The man, believed to be in his 40s, also tried to drive his car into the grounds of the prime minister's office but was blocked by a fence, NHK said.
He then reportedly tried to throw what appeared to be a smoke bomb but was stopped by police officers on the scene, who detained him.
The man was arrested on the spot on suspicion of obstructing public order, according to the reports citing police.
"The motives of the perpetrator are not known, but free speech must not be silenced by violence, and I am outraged by this act, as elections which are the very foundation of democracy are under way," said Hiroshi Moriyama, secretary general of the ruling Liberal Democratic Party (LDP), according to media.
The incident took place shortly before 6 am (2100 GMT Friday), the reports said.
Several plastic tanks were found in the man's small white car, according to the Asahi Shimbun daily and other media outlets.
Images from the aftermath of the incident showed a dark blue riot police van whose front panel had been burned away, as firefighters and police officers gathered at the scene.
Japan will hold a general election on October 27 in a test for new Prime Minister Shigeru Ishiba, who took office after winning the LDP's leadership vote last month.
Violent crime is rare in Japan, which has strict gun control laws.
But the country was shaken in 2022 by the assassination of former prime minister Shinzo Abe, who was shot in broad daylight on the campaign trail by a man with a makeshift gun.
Ishiba's predecessor Fumio Kishida was also targeted in 2023 by a man who threw an apparent homemade pipe bomb towards the then-premier, who was unharmed in the incident.
The conservative LDP has been in power for most of Japan's post-war history, albeit with frequent leadership changes.
Low voter turnout and a divided opposition mean the party and its junior coalition partner are likely to win this month's election, although the size of their majority could drop.
Former defence minister and self-confessed security policy "geek" Ishiba, 67, called a snap election to shore up his mandate for policies that include plans to "re-create" ageing Japan by revitalising depopulated rural areas.
