The painting by artist Fabian Chairez depicts Zapata virtually naked, wearing only a pink hat and stiletto heels, and sitting on a white horse with erect penis.
The painting's critics believe that it downgrades Zapata, who led the uprising for farmers and farmers' rights during the Mexican Revolution in the early 1900s.
About a hundred protesters stormed into Palacio de Bellas Artes, Mexico's premier cultural center, on Tuesday, screaming “burn it! burn it! ” Many then stayed and demonstrated outside the museum for several hours.
Some of them shouted homophobic bells, which caused another group to gather for a counter-demonstration.
The painting is shown as part of an exhibition in memory of Zapata, who died 100 years ago.