Two children suffered fracture in legs and one had head injuries, police said adding the school balcony collapsed due to torrential overnight rain.
A case had been registered and the owner of the middle school had been arrested, DSP (Phalodi) Murlidhar Kiradu said.
"The classes were in progress when the balcony collapsed injuring 20 students," he said adding the children were aged between 10 and 15 years.
Seventeen were admitted to a hospital in Phalodi and three were referred to Jodhpur for treatment, he said.