"Liberty Leading the People," painted by Eugene Delacroix in 1830, was tagged with "AE911" with indelible black marking pen, France 24 reported Friday.
French media speculated the writing could refer to a group known as "Architects and Engineers for 9/11 Truth," which contends the destruction of the World Trade Center towers on Sept. 11, 2001, couldn't have been caused only by airliners flying into them.
The 2.5-inch inscription was scrawled on the painting just before closing Thursday at the Louvre's new museum in Lens, Radio France Internationale reported.
She was immediately grabbed by another visitor and a museum guard.
A restorer is working to remove the graffiti.
The painting depicts Liberty as a bare-breasted woman carrying the French flag in one hand and a musket in the other. Delacroix painted it after three days of insurrection in July 1830.
The image was reproduced on 100-franc bills from 1978-95.