The former Dunedin swimmer, who relocated to Auckland earlier this year, was disqualified after being deemed to have moved on the blocks in her heat at the World Aquatics Championships in Singapore.
Fairweather, 21, finished fourth in her heat in a time of 4min 03.39sec.
It would have qualified her sixth for the final, but the small movement prior to the start meant she was out.
The false start has been labelled rare in an individual race, and even sparked online debate.
Canadian teenage sensation Summer McIntosh powered away to a convincing win in the final, clocking 3min 56.26sec to finish two seconds ahead of China's Li Bingjie.
American Katie Ledecky followed in third, while Australian Olympic champion Ariarne Titmus was not present.
Fairweather won the event at last year's World Championships, although the big three of Titmus, McIntosh and Ledecky did not feature on that occasion.
She came within a whisker of that trio at last year's Paris Olympics, finishing an agonising 0.26sec behind bronze medallist Ledecky.
Fellow New Zealander Eve Thomas also swam in the event, although missed out on a final spot, posting the 14th fasted heat time of 4min 10.10sec.
Fairweather will get her chance at redemption in the 200m freestyle tomorrow, and the 800m freestyle later this week.
- APL
