Laura Kenny and Kirsten Wild were both eliminated earlier than anticipated in the third discipline of the omnium.
The USA's Jennifer Valente maintained her place at the head of the field after a dramatic elimination race, though Japan's reigning world champion Yumi Kajihara remains a home hope just two points behind in second.
In a major set back to her medal hopes, Great Britain's Kenny was caught out early and eliminated seventh.
Tokyo 2020
Kenny misses out on medal as USA's Valente claims outstanding omnium victory
08/08/2021 AT 04:36
And there was another surprise two riders later as Wild, of the Netherlands, failed to time her sprint correctly and also exited before the halfway stage, with Clara Copponi taking victory for France.
"She was caught at the bottom with nowhere to sprint," Eurosport and discovery+ commentator Joanna Rowsell said of her former teammate Kenny's elimination.
This is normally her speciality. Let's hope she is ok.
The result leaves Kenny down in 13th with extremely slim hopes of a medal, needing a miracle at the Izu Velodrome in the points race to overturn a mammoth deficit.
Nineteen riders started the elimination race with Belgium's Lotte Kopecky not starting after stepping off her bike in the tempo race.

Britain's Laura Kenny, Ireland's Emily Kay, France's Clara Copponi and Belgium's Lotte Kopecky crash during the women's track cycling omnium scratch race during the Tokyo 2020 Olympic Games at Izu Velodrome in Izu, Japan, on August 8, 2021.

Image credit: Getty Images

Tatsiana Sharakova of Belarus was the first rider eliminated, while there was a big shock as Annette Edmondson (Australia) exited second after getting her positioning all wrong.
After the drama of Kenny and Wild's elimination, Valente appeared in cruise control as she made the final group of four.
But sharp work from the other trio with her, including Kajihara, knocked the leader out three laps from the finish.
Amalie Dideriksen of Denmark was the penultimate rider knocked out, leaving Kajihara and Copponi to duel.
And it was the Frenchwoman who took victory to vault herself back towards the top of the leaderboard.

‘It's not over yet for Laura’ – Wiggins on Kenny hopes after scratch race crash

Valente leads on 110 points, two clear of Kajihara on 108. Anita Stenberg (Norway) has 94, with Dideriksen now in close attendance two further back.
Wild's strong opening pair of performances leave her within touching distance at 90 omnium points, with Copponi perhaps the most distant realistic medal contender on 80.
The points race is contested over 80 laps with 80 sprints.
Riders can earn 20 points for lapping the field, which would be Kenny's only hope of claiming what would be a remarkable medal.
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Tokyo 2020
Kenny surges back into omnium contention with dominant tempo race victory
08/08/2021 AT 02:24
Tokyo 2020
'She's angry but didn't look too bad in terms of injuries' - Wiggins on Kenny's omnium crash
08/08/2021 AT 02:09