"The worst thing for an artist is when his work vanishes," Hörl told the DPA news agency.
He said he was also bothered by the lack of respect for his work.
The small sculptures were installed in mid-July, including in Salzburg's Mirabell Gardens, a tourist hotspot, to mark the 270th birthday of Austrian composer Wolfgang Amadeus Mozart.
The exhibition was organised in co-operation with the Mozarteum Foundation.
Hörl said he did not assume that holiday-makers had taken the 50-centimetre-tall Mozarts.
"This is organised theft," the artist said.
The plastic figures were likely stolen at night from the public park when the Mirabell Gardens are locked.
"I find it a bit cheeky," he said.
But it wasn't a million-euro heist.
Hörl said he would have sold the mini Mozarts for 90 euro ($A150) each after the end of the exhibition, meaning his total losses are about 20,000 euro.
Because the manufacturer of the sculptures is on holiday, replacement Mozart figures cannot be installed.
A few dozen can still be viewed until the end of August at the Mozarteum and at Mozart's birthplace in Salzburg.
Hörl is known for his installations featuring mass-produced figures of famous personalities.
He installed small armies of Schillers, Goethes and Hölderlins in German cities.
There was also an incident like the one in Salzburg.
During a campaign in Bayreuth, 100 figures of composer Richard Wagner were stolen.
