Maglev train operator Central Japan Railway Company (JR Central) says one of its seven car trains hit a top speed of 603kph (375mph), and managed nearly 11 seconds at faster than 600kph.
The new record came less than a week after the company recorded a top speed of 590kph, breaking its own 2003 record of 581kph.
The maglev hovers 10 centimetres above the tracks and is propelled by electrically charged magnets.
About 200 train buffs gathered to witness the record-setting run, with the crowd cheering as the train broke through 600 kph per hour mark.
“It gave me chills. I really want to ride on the train,” an elderly woman told public broadcaster NHK as the carriage rocketed past her.
“It’s like I witnessed a new page in history.”
Yasukazu Endo, who heads the maglev test centre southwest of Tokyo, said: “The faster the train runs, the more stable it becomes – I think the quality of the train ride has improved”.
JR Central wants to have a train in service by 2027 on the route between Tokyo and the central city of Nagoya – a distance of 286km.
The service, which will run at a top speed of 500kph, is expected to connect the two cities in only 40 minutes, less than half the present journey time on Japan’s already speedy bullet trains.
By 2045, maglev trains are expected to link Tokyo and Osaka in just one hour and seven minutes, slashing the journey time in half.
However, construction costs for the dedicated lines are astronomical. They are estimated at nearly $100 billion for the stretch to Nagoya, with more than 80 per cent of the route expected to go through costly tunnels.
Japan is looking to sell its Shinkansen bullet and maglev train systems overseas, with prime minister Shinzo Abe acting as a travelling salesman in his bid to revive the Japanese economy partly through infrastructure exports.
He is due in the United States this weekend, where he will be touting the technology for a high-speed rail link between New York and Washington.
Last year, Mr Abe took US ambassador to Japan Caroline Kennedy on a test ride.
“This technology is something that will bring great benefits to Japan and hopefully the United States one day,” Ms Kennedy said.
The maglev train is a contender for president Barack Obama’s multi-billion-dollar national high-speed rail project.
Mr Abe said Japan would not charge licensing fees in the US for the train, a strong incentive for Washington to select the system for a high-speed rail line between Washington DC and Baltimore.
The proposed 60km link would represent the first phase in the government’s plan to connect the capital and Boston.
Japan started its study on the maglev train system as a national project in 1962 and succeeded in running at a speed of 60kph a decade later.