The court also asked the state to submit an amended indictment against Vanunu within a month, his lawyer Avigdor Feldman said on Monday.
Vanunu was released from prison last year, after serving an 18-year term for treason, for spilling Israel's nuclear secrets. The conditions of his release included a ban on foreign travel and meetings with foreign reporters.
Two months ago, he was indicted on charges he violated those restrictions.
In a ruling on Sunday, Jerusalem Magistrate Yoel Tzur said the West Bank and Gaza Strip cannot be considered outside Israel because they can be reached without a passport or visa.
He also told prosecutors to be more specific about Vanunu's alleged violations of a ban on meeting foreign journalists.