Majd Kayyal, aged 23, from the northern coastal city of Haifa, crossed into Jordan on 23 March and travelled on to Lebanon for a conference organised by As-Safir newspaper, Israel's Shin Bet domestic security agency said.
A Shin Bet spokesperson stressed Lebanon is defined as "an enemy country" and Israelis are prohibited from visiting.
"A suspicion arose that he was recruited by a hostile organisation, and therefore upon his return on 12 April he was arrested by police and taken to us for questioning," she told AFP.
Public radio said Kayyal was suspected of contacts with the pro-Syrian Shi’ite militant group Hezbollah, an arch foe of Israel.
The spokesperson said Kayyal had arranged the paperwork to enter Lebanon through the Palestinian Authority in the West Bank city of Ramallah.
Kayyal had been already questioned by security services in 2011 for having taken part in an aid flotilla to the besieged Gaza Strip, she said.
Speaking to AFP, Kayyal's mother Suhair Badarni said he worked for As-Safir, a leading pro-Syrian Beirut daily, and that the family "did not consider Lebanon an enemy country".
"They are trying to prevent us from contact with our Arab surroundings," she said. "Israeli Jewish reporters have gone to Lebanon and Syria who haven't been investigated."
Kayyal's arrest was placed under a gag order, which an Israeli court lifted on Thursday.
Arab Israeli rights group Adalah said the gag order was to prevent public debate about "the prohibition on Palestinian citizens of Israel from entering numerous Arab countries".
Adalah, which also employs Kayyal, said "the crimes for which Kayyal is accused are essentially carrying out his duty as a journalist, and his rights to freedom of movement and freedom of expression."
The Shin Bet spokesperson said the agency would decide in coming days how to proceed with the investigation and charges of "entering an enemy country".