The 24-year-old was Japan's best hope for a swimming gold medal next
year alongside Olympic poster girl Rikako Ikee, who was diagnosed with
leukaemia last month.
"I've been unable to achieve the results I had hoped for since the 2017 season," Hagino said in a statement.
"As the gap between my targets and reality has widened, it has become harder for me to maintain my motivation."
The former Asian champion has struggled with form since capturing
gold in the men's 400 metres individual medley at the 2016 Rio Olympics.
Japan coach Norimasa Hirai admitted that Hagino was in no shape to
contest the nationals in Tokyo after skipping another local meet last
"In his current condition it would be really hard," Hirai told Japanese media.
"He's not in very good spirits. He needs to rest and when he decides to comes back, he needs to start swimming for himself."
Hagino shot to fame by scooping four gold medals at the 2014 Asian
Games, including a stunning upset over Chinese giant Sun Yang in the
He stormed to victory in his pet 400m individual medley in Rio and added a silver behind Michael Phelps in the 200m.
But Hagino has lost his mojo since, his alarming slump in form
coinciding with American Chase Kalisz's emergence as the world's premier
medley swimmer and the hot favourite for gold at the 2020 Tokyo
"The ball is in his court," shrugged Hirai, asked when he thought Hagino would return.
"Nothing has been decided - it's a clean slate, only he knows," he
added after Hagino's appearance at this summer's world championships in
South Korea was also plunged into doubt.
"It's obviously not a plus that he's not entered the nationals. It's a critical situation for him but he has to stay positive."
Hagino, who also opted to miss a recent Japan training camp in Spain,
added: "I'm still not mentally ready to compete at full strength. I
humbly apologise to swimming fans and am prepared to accept any
criticism that comes my way."
Ikee sent shockwaves through the sport when she tweeted that she had
been diagnosed with leukaemia after cutting short a training camp in
The 18-year-old, who bagged a record six gold medals at last year's
Asian Games in Jakarta, had been tipped to push for Olympic gold on
several fronts in her home city, in particular in the women's 100 metres