The 62-year-old former nuclear technician was jailed in 1986 for disclosing the inner workings of Israel's Dimona nuclear plant to Britain's Sunday Times newspaper.
He spent more than 10 years of his sentence in solitary confinement.
Israel is the Middle East's sole if undeclared nuclear power, refusing to confirm or deny that it has such weapons.
Upon his release in 2004, Vanunu was slapped with a series of restraining orders, forbidding him from travel, contact with foreigners or speaking to media.
He has twice been jailed for breaking those orders.
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In January, Vanunu was convicted of meeting with two US nationals in Jerusalem in 2013 without having permission to do so.
Monday's appearance was a sentencing hearing over that conviction.
His lawyer told the court it was a chat lasting "minutes" in a coffee shop with doctors visiting Israel.
He was cleared of two other charges, one of which related to an interview he gave to Israel's Channel 2 television in 2015.
"I left prison and they put me in another prison," he told Jerusalem magistrates court. "I performed my punishment and they keep on punishing me."
The court did not pass sentence or set a date for sentencing, but Judge Yaron Mientkavich said he would consider ordering him to perform community service.
Vanunu told AFP outside the courtroom that he had been confident that he was not returning behind bars.
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"I knew there was no chance I would be going back to prison because they didn't find me guilty on all the charges," he said.
He added that more than 30 years after he worked in the nuclear plant he had no more to reveal to anybody.
"All the nuclear secrets have gone," he said in English. "I don't have any nuclear secrets, and everything is on the internet."
"After 18 years in prison it's enough and more... they should let me go. All what I want is freedom, that's all."
Israel has refused to sign the nuclear Non-Proliferation Treaty or to allow international surveillance of its Dimona plant in the Negev desert of southern Israel.
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