The 50-year-old former technician was released last April after serving an 18-year term for giving secrets about the Dimona nuclear reactor to a British newspaper.
His revelations led experts to conclude that Israel had nuclear weapons.
"It is shameful to Israeli democracy to bring me back to court after all those years in prison," Vanunu told journalists outside the Jerusalem court. "This case is proving to the world that Israel is not a real democracy.
"As a human being, I have the right to express my political views and my ideas. I have no more secrets," he said.
Terms of freedom
Under the terms of Vanunu's release, he was forbidden from speaking to foreign media and had to remain inside Israel. If convicted of violating the bans, he can be jailed for up to two years.
Vanunu did not enter any plea in court as his lawyer challenged the validity of the case. The next hearing is due on 19 May.
The bans are due to be reviewed this month. The Justice Ministry said in a statement that an extension was being considered but that Vanunu would be allowed to plead his case and a final decision had yet to be made.
"Let me leave, let me go. Enough," Vanunu told reporters.
An indictment filed in a Jerusalem court last month charged him with 21 counts of violating the restrictions.
Listing interviews in the US, British, Australian and French media, the indictment quoted Vanunu as saying Israel had assembled hydrogen and neutron bombs at Dimona and was annually producing 40kg of plutonium, enough to make 10 atomic bombs, at the facility.
Last November, police arrested Vanunu, a convert to Christianity, at the Jerusalem church where he has lived since he left jail and brought him to court on suspicion of having spilled more state secrets to the foreign press.
He was later released to house arrest and has remained under constant surveillance by Israeli security services.
The indictment also charged him with violating a ban on travel overseas or to the occupied Palestinian territories. Vanunu was briefly detained by Israeli police after he tried to visit the West Bank town of Bethlehem last Christmas.
Vanunu was abducted in Rome by agents of Israel's Mossad intelligence service and jailed in 1986 for discussing his work at the Dimona reactor with Britain's Sunday Times.