The work "dirty corner" by Anish Kapoor was found sprayed with yellow paint on Wednesday and is now being cleaned by palace authorities.
"If this act of vandalism means anything, it speaks more to a certain intolerance in France than to art itself," Kapoor said in an interview with Le Figaro daily.
"The problem seems more political than anything else," he added.
The 60-metre (200-foot) long, 10-metre (33-foot) high steel-and-rock abstract sculpture by the British-Indian sculptor, resembling a funnel in the form of an orifice, is set up in the garden aimed directly at the royal chateau, which attracts five million tourists a year.
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Some French media outlets have expressed unease at the level of provocation unleashed by Kapoor.
No one has claimed responsibility for vandalising the sculpture.
French Culture Minister Fleur Pellerin said the vandalism was "an attack on the freedom to create" and stressed "all my support to the artist.