Net Khai, 37, faces up to a year in jail after being charged with "producing and distributing pornographic images'' by Phnom Penh Municipal Court, prosecutor Ek Chheng Huot said.
He was arrested at his pagoda in the Cambodian capital on Saturday over allegations that he secretly taped the women pouring sacred water over themselves in a pagoda bathroom, said police chief Touch Naruth.
Net Khai was arrested after a victim approached police and said that video clips showing the naked women had been shared among people via their mobile phones in recent weeks.
He was subsequently stripped of his religious status.
"He has filmed hundreds of women since 2008. They came to the monk to be blessed with holy water, but they were secretly filmed," Touch Naruth said.
"His act affects other monks and Buddhism and seriously harms our tradition," he said, adding that Net Khai had confessed to his crimes.
Police said they were looking for the man's accomplices.