In a rare appearance before the Knesset's foreign affairs and defence committee, Meir Dagan said Iran was now close to the "point of no return" in developing nuclear arms.
The program was "the biggest threat to Israel's existence since its creation" in 1948, he was quoted as saying.
The warning comes just three days before the United Nation's nuclear watchdog, the International Atomic Energy Agency (IAEA), is to decide whether to haul the Islamic republic before the UN Security Council for hiding sensitive aspects of its nuclear programme.
Dagan also said that Israel had discovered in the last three months that Iran was close to finishing construction of a uranium enrichment plant in the central Kachan area which could eventually give it the capacity to build around a dozen nuclear bombs.
Iranian President Mohammed Khatami announced last February that a nuclear power plant would be built in Kachan after the discovery of a uranium mine in the region.
During a visit to Washington last week, Israeli Defense Minister Shaul Mofaz also warned that Iran would reach a "point of no return" in its nuclear program within a year unless there were concerted efforts to stop it.
"Concentrated efforts are needed to delay, to stop or to prevent the Iranian nuclear program," he said in a speech.
The IAEA released a report last week accusing Iran of conducting two decades of covert nuclear activities, including plutonium manufacture, although it said there was no evidence as yet that it was trying to build a nuclear bomb.
The Security Council could slap punishing sanctions on Iran, but US hopes of this dimmed on Monday with Europe's top diplomat, EU foreign policy chief Javier Solana, saying Iran had been "honest" in its nuclear dealings with the international community and did not deserve such action.
Since the collapse of Saddam Hussein's regime in Iraq, Israel has come to regard the Islamic fundamentalist administration in Tehran as its number one enemy.
Iran's former foreign minister Ali Akbar Velayati, now a top advisor to supreme leader Ayatollah Ali Khamenei, was quoted as saying last week that the mere existence of Israel is contrary to Tehran's national interests.
Iran refuses to recognise Israel and top officials frequently call for the destruction of the Jewish state. But Tehran denies giving material support to Palestinian militants who have waged a bloody campaign for the past three years against Israeli military occupation in their territories.
During a major military parade on September 22, the Islamic republic showed off six of its Shahab-3 missiles which were decorated with anti-Israeli and anti-US slogans, including one saying Israel should be "wiped off the map".
Israel has warned that the new ballistic missile represents a threat to the whole of the Middle East.
Israel, like the United States, accuses Iran of using a civil atomic energy program as a cover to develop nuclear weapons. It also accuses Iran of giving support to the Lebanese-based militia Hezbollah and Syria.
Israel's army chief of staff General Moshe Yaalon warned at the weekend that more action could be directed against Syria if it "ignores the message" of last month's air strike near Damascus aimed at an alleged Palestinian militant training facility.
He accused Syrian President Bashar al-Assad's regime of allowing Hezbollah to launch attacks against Israel from neighbouring Lebanon.