The 33-year-old, who has been Japan skipper since 2010, arrived in the UAE late on Sunday despite his Bundesliga club saying he needed an operation on a knee injury sustained in a 3-0 defeat by Bayern Munich on March 11.
On Monday, though, the midfielder said he had travelled to join the squad with the blessing of Eintracht but would now go to Japan to get another diagnosis of the injury.
"There is a good chance I will go under the knife. I'll return to Japan for a third opinion with a trusted doctor," Hasebe told reporters in Al Ain according to Kyodo news.
"I'm leaving the team just before this crucial match and I feel really bad. Obviously, I am very disappointed and it has been a very difficult decision to make.
"But I don't think this will have too much of a negative impact on the team. I trust my team mates 100, 120 percent."
Japan are second in Group B of Asia's qualifying tournament for the Russia 2018 finals, level on points with Saudi Arabia and one ahead of third-placed Australia and the UAE. Only the top two teams are guaranteed to qualify for the finals.
KEY FIGURE
Hasebe has been a key figure for Japan for much of the last decade, helping the team win the 2011 Asian Cup and qualify for the 2010 and 2014 World Cups.
"Hasebe is a very strong captain for us," said coach Vahid Halilhodzic when he announced his squad last week. "Having a team without him in it is unthinkable."
The former Urawa Red Diamonds stand out was injured when he collided with a post while clearing a Thomas Mueller shot off the line against Bayern.
He was taken to hospital after the game to have a wound on his left shin stitched but later broke down in training and the club decided he would need an operation.
Halilhodzic, who took over as Japan coach following Javier Aguirre's departure in early 2015, has been under pressure following several unconvincing displays, including a shock 2-1 loss to the Emirates in the opening match of the round.
"Ever since losing the first game against the UAE at home I have wanted to come here and erase the disappointment of that defeat," Hasebe added.
"I have played well with my club with that feeling in mind and to get this injury just before the game is heartbreaking."
Japan, who are seeking a sixth straight appearance at the World Cup, take on the UAE on Thursday before returning home to face Thailand on Tuesday.
(Reporting by Nick Mulvenney in Sydney, editing by Ken Ferris)
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