The apparently random attack took place at around 9:50 p.m.in the 12th auto of the Nozomi No. 265 bound for Shin-Osaka Station from Tokyo, which had just departed with 880 passengers aboard.
Police arrested the 22-year-old unemployed suspect on suspicion of attempted murder, the report said.
According to the publication, the man of 30-40 years old, was shot in the neck and later died in hospital, two women were injured in the head.
News reports said two women who appeared to be in their 20s were wounded but their injuries were not life-threatening.
The offender was detained by the police. The police seized a weapon when they arrested Kojima.
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We will remind, on April 27 in North China unknown armed with a knife attacked a group of 19 children near one of the schools in Shaanxi province.
According to the Kanagawa Prefectural Police, Kojima started by allegedly attacking the woman sitting next to him, before proceeding to attack a woman on the other side of the aisle.
The suspect told investigators that he felt "frustrated and wanted to kill someone", public broadcaster NHK said, adding that he used at least two knives. She had been calling his mobile phone recently but could not reach him.
The train was carrying more than 800 passengers at the time of the incident. There were around 880 passengers aboard the Nozomi 265, the day's last train bound for Shin-Osaka, according to Central Japan Railway Co., also known as JR Central.