General Ahmad Vahidi issued a statement warning Israel that an attack would lead to the collapse of the Jewish state.
The warning on Iran's state-run Press TV website came after a UN report said Iran had tripled its production rate of enriched uranium over the past three months.
The confidential report to member states, seen by the Guardian, also states that Iran is refusing to co-operate with an investigation into evidence that the country may have worked on designing a bomb.
Meanwhile diplomatic experts have warned that a pre-emptive attack on Iran's nuclear sites by Israel could draw the US into a new Middle East conflict.
"Israel can commence a war with Iran, but it may well take US involvement to conclude it," said Karim Sadjadpour, a Middle East specialist at the Carnegie Endowment for International Peace.
Iran's warning follows increasingly tough rhetoric from Israel about the need to halt Iran's nuclear development.
Israeli officials believe a pre-emptive strike must happen before the summer because Tehran is moving more of its nuclear installations underground.
The International Atomic Energy Agency (IAEA) found that much of the increased production of uranium, enriched to the level of 20%, had taken place at an underground site known as Fordow.
Tehran has said it needs the material for its research reactor, which produces medical isotopes, but western governments argue that its stock of enriched uranium brings it significantly closer to weapons-grade fissile material.
The IAEA inspectors also found that Iran had stepped up the installation of centrifuges at its main uranium enrichment plant in Natanz. Over the past three months, 2,600 new centrifuges have been brought into operation, spinning uranium gas.
The report found that Iran had now produced nearly five and a half metric tonnes of low enriched uranium – enriched to about 3.5% – and about 109kg of uranium enriched to 20%. If enriched further, to more than 90% purity, the total stockpile would be more than enough to make four nuclear warheads.
Iran says it has no intention of making weapons, and the report may not be enough for western countries, led by the US, the UK and France, to persuade Russia and China to take part in an escalation of sanctions.
The Russian prime minister, Vladimir Putin, said the focus on the nuclear programme was a cover for western attempts to oust the clerical regime in Tehran.
But Israel worries that Iran could soon enter a "zone of immunity" in which enough of its nuclear materials are beyond the reach of Israeli air power that it cannot be stopped, or can be stopped only by superior American firepower.
If Israel's American-made strike planes managed to penetrate Iranian air space and bomb Iran's main nuclear facilities, some of which are underground, then Iran would be expected to retaliate.
Barack Obama has not ruled out using force to stop Iran from building a bomb. But his administration, joined by many allied nations, has counselled Israel to hold off.
Obama is due to meet the Israeli prime minister, Binyamin Netanyahu, at the White House on 5 March.