However, the authorities denied any loss of life, but said that 48 people had been injured, including 28 police officers.
"The Rabat chief prosecutor's office ordered detectives to hold a preliminary investigation following the broadcast Saturday, by Al-Jazeera from its Rabat bureau, of information stating that there had been deaths during demonstrations in Sidi Ifni," the source said.
"Upon completion of the investigation, carried out in accordance with the law, Hassan Rachidi and Ibrahim Sebaa El Layl have been charged with publishing false information and conspiracy, under the terms of article 42 of the press code."
Their trial is to be held on July 1 in Rabat.
Surprise over decision
The Moroccan communication ministry also announced that it had withdrawn Rachidi's media accreditation in the country.
"I am very surprised by this decision, but I believe [the authorities] want the head of the [Al-Jazeera] bureau chief," Rachidi said.
"We received the information [of the deaths] from a well-respected human rights association which had given a press conference to announce the news."
In May, the Moroccan government stopped Al Jazeera from broadcasting a daily news programme covering countries in and around North Africa from its studios in Rabat.