Japan became the last member of the Group of Seven leading industrialised nations to begin its vaccination drive against COVID-19 on Feb 17.
It has so far received three shipments of vaccine developed by Pfizer Inc and BioNTech, comprising around 1.4 million shots.
The Pfizer/BioNTech vaccine has to be stored at a temperature of around minus 75 Celsius (minus 103 Fahrenheit).
A medical institution reported that the freezer malfunction had occurred over the weekend, rendering 172 vials of the vaccine, or 1,032 doses, useless, the ministry said.
It declined to identify the name of the medical institution or the manufacturer of the freezer in question, but said the freezer maker would start looking into the cause of the malfunction.
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