The 20-year-old, already being tipped to win medley gold at the 2016 Rio Olympics, clocked four minutes, 18.77 seconds in the heats to qualify second quickest behind team-mate Daiya Seto.
Seto, who won the men's 200m butterfly on the opening day in Incheon, swam 4:15.94. (Hagino Completes Golden Treble)
"Daiya's put up a good time so I'm looking forward to the final," Hagino told reporters, the morning after taking silver behind China's Sun Yang in an epic 400m freestyle final.
"Hopefully I can do enough to beat him and win gold in a quick time," added the Japan sensation, who scored a shock win over Sun and South Korea's Park Tae-hwan in the 200m freestyle at the weekend.
After a hot start in the pool, Japan find themselves playing catch-up to China, who captured six titles in Tuesday's finals to lead the gold medal standings 11-7 over their fierce rivals at the midway point of the six-day pool competition.
Japan's Natsumi Hoshi, silver medallist at last month's Pan Pacific championships, was the fastest qualifier in the women's 200m butterfly in 2:13.64.
Defending champion Jiao Liuyang of China was third quickest with 2008 Olympic champion and world record holder Liu Zige fourth in 2:14.38.
Japan's Yasuhiro Koseki, Olympic great Kosuke Kitajima's heir apparent, bounced back from a hugely disappointing swim in Tuesday's 200m breaststroke to record the fastest time in the 100 heats in 1:01.39.
"Yesterday was a good learning experience for me," said Koseki, who had fought back tears after finishing with the bronze in his signature 200 behind surprise winner Dmitriy Balandin of Kazakhstan.
"I was thinking too much about the race and got tight. I've snapped out of it and am ready to swim loose and hopefully put up a fast time."
Balandin was second in 1:01.55 just ahead of Uzbekistan's Vladislav Mustafin.
China have dominated the Asian Games swimming in recent years, winning 24 of the 38 golds at Guangzhou in 2010 but Japan have provided a sterner test this year.