Naoko Takahashi will not defend her Olympic marathon title later this year after being left out of Japan's team for Athens.
Takahashi powered to victory at the Olympics in Sydney
Reika Tosa was selected in the third and final team spot following her victory in Nagoya at the weekend.
Tosa will join Mizuki Noguchi and Naoko Sakamoto at the Games in August.
Takahashi, who won gold at the 2000 Sydney Olympics, suffered a shock loss in Tokyo last December - the first time she had been beaten since 1998.
The 31-year-old finished runner-up in Tokyo in the first of three Athens
qualifiers for Japanese athletes, losing to Ethiopian Elfenesh Alemu in an
ordinary time of two hours, 27 minutes and 21 seconds.
The defeat sparked national debate and the athlete decided to leave her fate in the hands of the Japan Amateur Athletics Federation (JAAF).
But failure to appear at subsequent qualifiers in Osaka or Nagoya gave Japanese selectors little option but to drop Takahashi.
She told a media conference: "Going to Athens was always a major goal and I imagined myself running there, so it's a shame.
"Part of me thinks I should have run the qualifying events
but the decision not to was mine, so I have no regrets. This does not mean I am done with athletics."
JAAF official Keisuke Sawaki said: "Of course, we know Takahashi is a quality athlete but [in Tokyo] she went out very fast and struggled at the end.
"It was a very tough decision to make but stamina is an important factor to consider in major competitions."
Sakamoto triumphed in the Osaka international marathon in January, while Noguchi qualified for the Japanese Olympic team by virtue of her silver medal at last year's World Championships in Paris
Masako Chiba, who took bronze behind Noguchi, was named reserve for Athens by the JAAF.