Israeli naval commandos seized the vessel on Wednesday in the Red Sea between Eritrea and Sudan, with the military saying it was carrying an Iranian shipment of M-302 rockets destined for the Hamas-run Gaza Strip.
The Panamanian-flagged Klos-C was escorted into Eilat port by two Israeli warships.
Thousands of Israelis gathered on a hill overlooking the port broke into applause when the ship came into view.
"We will dismantle all the containers to verify if they contain other weapons," an army spokesman said, adding that a news conference will be held at the end of operations late on Monday.
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This, the radio said, "will prove to the world that Iran is providing weapons to terrorists active in the Gaza Strip".
Iran has flatly denied any involvement with the shipment, which the Israeli army said was carrying missiles capable of striking anywhere in Israel.
At the time of the vessel's capture on Wednesday, military spokesman Brigadier General Motti Almoz told army radio that dozens of the M-302 long-range missiles were on board.
"There is clear and unequivocal information that this (shipment) came from Iran," Almoz said, without elaborating.
Iranian Foreign Minister Mohammad Javad Zarif accused Israel of lying and noted that the announcement of its capture coincided with a speech by Israeli Prime Minister Benjamin Netanyahu at the AIPAC pro-Israeli lobby in the United States.