Of the 34,500 works of art belonging to the city, the whereabouts of 946 are unknown, lost over the years due to lackadaisical management, reported Tages Anzeiger.
The most significant loss is a painting by Swiss-French artist and architect Le Corbusier, dating from 1927, which has an estimated value of 1.5 million francs.
Zurich city authorities obtained the painting in 1964. It was initially displayed in a maternity hospital, before being put into storage. It later disappeared, probably in the 1990s, authorities told the media.
Considerable effort has been made to find it, Marc Huber, a spokesman for the city's construction department, which is responsible for the art collection, told the Tages Anzeiger.
In 2007 the city lodged a complaint with police, and the artwork was entered into an international database of lost and stolen artworks, but as yet it hasn't been found.
The department has now published a list of the missing artworks in order to try and get them back.
After the piece by Le Corbusier the next most valuable is probably worth around 10,000 francs said Huber. He estimated the total value of the missing art to be around two million francs.
The artworks were most likely lost due to mismanagement, said the paper. Over the years many were loaned out without being properly documented or tracked.
It wasn't until 2009 that the city took a proper inventory of its artwork, despite starting the collection a century earlier.
The authorities now have stricter controls which have prevented more going missing, and several dozen missing artworks have been recouped in recent years, six in 2017 alone, Huber told the Tages Anzeiger.
Zurich isn't the only the place to suffer such embarrassment.
According to Le Matin some 2,000 works are missing from the Zurich cantonal collection, while the city of Bern has misplaced up to 200 artworks.
Other cities have remained tight-lipped about the extent of their art collections, said the paper.