The container, which can hold 12,000 tonnes of the corrosive liquid, made headlines last year when Hassan Nasrallah, leader of Lebanon's Shiite militia Hezbollah, said it would go off like "a nuclear bomb" if hit by his group's missiles.
Nasrallah, whose rockets pounded the northern city in a 2006 war with Israel, echoed warnings from experts and activists in the Israeli media that "tens of thousands of people" would be killed if the container was struck.
But the Haifa district court threw out the appeal, saying the tank could cause "a disaster of national scope" affecting thousands of people.
The Wednesday ruling comes after a decades-long struggle by environmental groups opposed to the tank in Haifa's densely-populated bayside area.
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