"Vanunu was arrested [for] a relationship between a man and a woman, with a Norwegian citizen," he said.
"He is not being accused of giving any secrets. She is not interested in nuclear business - she's interested in Mordechai Vanunu [and he] is probably interested in her."
Vanunu was sentenced to six months in jail in 2007 for violating the ban on contact with foreigners.
Vanunu was jailed as a traitor after he leaked details and pictures of activities at the Dimona reactor to the UK-based Sunday Times newspaper in 1986.
The report led experts to conclude the facility had produced fissile material for as many as 200 atomic warheads, an amount that would make Israel the world's sixth largest nuclear power.
In court on Tuesday, Vanunu, who refuses in protest against Israel to speak Hebrew publicly, addressed reporters in English.
"This Jewish state has 200 atomic ... hydrogen bombs, atomic weapons, neutron bomb," he said.
"They are not able to say they have the bomb, they are not able to destroy anyone ... instead they arrest Vanunu Mordechai."
Israel refuses to confirm or deny whether it is the Middle East's only nuclear power under a policy of "strategic ambiguity", which it says wards off its enemies while preventing a regional arms race.