Four boxes containing the face masks disappeared from a locked storage facility at the Japanese Red Cross hospital in the western port city of Kobe, a hospital official said on Tuesday.
"We still have a large number of masks — enough to continue our daily operations at the hospital, but this is so deplorable," the official told AFP.
Police have launched an investigation as they suspect the thieves intend to resell the masks.
Masks have sold out at many drug and discount stores across the nation as the number of infections have increased in Japan — one of the most affected countries after China where the death toll from the virus has hit 1,800.
Public anxiety has been also fuelled by headlines of hundreds of people infected with the virus on board a ship quarantined off Japan.
The theft came after knife-wielding men jumped a delivery driver and stole hundreds of toilet rolls on Monday in Hong Kong, where the coronavirus outbreak has fuelled a run on face masks, hand sanitiser and toilet paper.
Japanese flea market app Mercari called on its users to trade masks "within socially accepted limits" after a box of 65 masks was priced at more than 50,000 yen ($456) at its online marketplace.
The Japanese government has "strongly requested" mask makers to boost output, Chief Cabinet Secretary Yoshihide Suga told reporters last week.
There has been a shortage of masks at drug stores in the hygiene-conscious nation where face masks have been part of everyday streetwear for decades.
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