Israel has resticted Vanunu's movements and personal contacts since he finished his first jail term.
Tel Aviv argues that Vanunu could leak new details on his past work at the Dimona nuclear reactor.
Vanunu was convicted in April of maintaining unauthorised internet contact with foreigners, including foreign newspapers.
He was also found guility of breaching prohibitions on entry to the occupied West Bank.
In addition to the six month jail term, the court also passed a six month suspended sentence.
The court said in its ruling that it would hold off on jailing Vanunu to allow him to appeal.
"While returning a man to prison after he served 18 years there does not bring joy to anyone, there was no other choice but to take this step to make clear that the nation will defend its secrets and protect its security," Dan Eldad, a prosecutor, said in a statement.
Since his release, Vanunu, a convert from Judaism to Christianity, has denied charges that he has more classified information that he could leak if he was allowed to emigrate.