"Narges Mohammadi has been charged with propagating against the Islamic Republic of Iran's system," the agency quoted Iranian judiciary spokesman Ali Reza Jamshidi as saying.
Jamshidi confirmed reports that Mohammadi has been banned from travelling and said she is due to appear in court, though he did not say when.
On May 10 Ebadi's rights group, the Human Rights Defenders Centre said on its website, that Mohammadi was barred from taking a trip to Guatemala to speak at a conference there on the role of women in democracy.
Mohammadi, deputy head of the centre, and another peace activist, Soraya Azizpanah, were stopped at Tehran's Imam Khomeini airport as they were headed to Guatemala, the group said.
Friday's IRNA report gave no details about Azizpanah.
The centre founded by five prominent human rights lawyers and headed by Ebadi, the 2003 Nobel peace laureate, has faced mounting pressure in recent months and its office was shut down in a police raid in December.
The centre's former secretary Jinous Sobhani was detained for about two months for links with the banned Bahai faith and released on bail in March.
Group members are outspoken critics of the human rights situation in Iran.
Several Iranian human rights activists have been barred from leaving the country to participate in international conferences or to collect prizes in the past two years.
In March last year, Iran barred feminist and journalist Parvin Ardalan from leaving the country to receive the 2007 Olof Palme Prize in Stockholm which she had been awarded for her campaign for equal rights for women in Iran.
