The art installation by Dutch artist Forentijn Hofman, featuring twin 18-meter (59-feet) inflatable ducks, was unveiled to the public on Friday.
The exhibition came a decade after one of Hofman's air-filled avians first visited the Chinese city, with the artist saying the new work would bring "double luck".
But organizers had to let the air out of one bird due to high summer temperatures, which on Saturday reached highs of 33 degrees Celsius (91.4 degrees Fahrenheit).
The "rubber duck skin had become strained because the hot weather has caused air pressure to rise," the organizers said in a statement.
The affected creature was drained of air to "avoid risk" and was pending repair, organizers said, leaving just one sitting duck in Hong Kong's Victoria Harbor.
Hofman's Rubber Duck series has made appearances in major cities since its 2007 debut, and made headlines in Hong Kong when it arrived in 2013.
That exhibit lasted 13 days before it, too, was deflated.