The former nuclear technician was charged by a court in Jerusalem for speaking to foreign media and defying a travel ban.
Vanunu, 50, served 18 years behind bars for revealing to a London newspaper that Israel was producing nuclear weapons and providing details of the workings of the Dimona nuclear plant.
“They charged me for giving interviews to the media and for not respecting the restrictions of my release. They’re not charging me with releasing secrets,” said Vanunu, speaking to AFP from his residence in east Jerusalem.
He did not appear in court. There is no warrant for his arrest and no date has yet been set for any trial.
Israel’s justice ministry charged Vanunu with 21 counts of violating the restrictions, some of which are due to expire next month.
“They can charge me 50 times if they want,” he told Reuters.
“I have not been charged with harming national security but with not respecting the restrictions on me,” he said.
“I am still hopeful they will end my restrictions.”
Vanunu, a Christian convert, said he will continue speaking to the media despite the charges.
The terms of his release last April stated he was forbidden from leaving Israel or speaking to foreign journalists without prior authorisation, amid fears he would leak further details relating to nuclear secrets.
“They want a trial but my lawyers are working on it. I’m not worried,” Vanunu said, adding that he expects to hear within weeks whether the matter will go to court.
He has been living at St George’s Anglican cathedral since his release, and said his asylum applications to a number of Western countries have been turned down.
He was last arrested in December as he tried to enter the West Bank town of Bethlehem to attend Christmas Eve midnight mass, and had to post bail of 50,000 shekels (A$14,495) and remain in Jerusalem.