Mr Muallem said: "Unfortunately, some official pirates in the seas, sometimes in the name of the navy, sometimes in the name of inspection, obstruct trade movement between Syria and Iran.
"This ship does not carry Iranian weapons to Syria and does not contain military material to manufacture weapons in Syria. This ship carries imported goods from Syria to Iran."
Iran and Syria are widely held to be the main sponsors of Hezbollah. The Shia group has not yet commented on the seizure.
The Antiguan-flagged vessel, Francop, was boarded near Cyprus, the military said, and has been towed to the port of Ashdod.
Containers piled three deep on its deck were opened and inside were rockets, hand grenades, mortars and at least 3,000 missiles, the Israeli military said.
Prime Minister Benjamin Netanyahu said the arms were intended to strike Israeli cities.
"Whoever still needed indisputable proof that Iran continues to send weapons to terror organisations got it today in a clear and unequivocal manner," he said.
The Israeli military said cargo certificates showed the ship had sailed from Iran and was bound for Syria, from where the weapons would be transferred to Hezbollah in Lebanon. However, the military did not show the documents.
Israel and Hezbollah fought a month-long war in 2006 during which about 1,200 people were killed in Lebanon and about 160 were killed in Israel.
The BBC's Middle East analyst Roger Hardy says that although Israel's northern border has been largely quiet since 2006, Israel and Hezbollah operate from the shared assumption that sooner or later the war will be reignited.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.