"The fact that a country like Iran, an enemy (of Israel) and which is particularly irresponsible, has equipped itself with non-conventional weapons is worrying," General Moshe Yaalon told military radio.
"The combination in this case of a non-conventional regime with non-conventional weapons is a concern," Yaalon said in an interview to mark the Jewish new year.
"At the moment there is ongoing international diplomatic activity to deal with this threat and it would be good if it succeeds.
"But if that is not the case we would consider our options," the general added.
Israel has come to regard Iran as its chief military threat since the downfall of Saddam Hussein's regime in Iraq.
It warned last month that a new ballistic missile that was officially inaugurated by Iran's supreme leader Ayatollah Ali Khamenei represented a threat to the whole of the Middle East.
Iran put on show its new Shahab-3 ballistic missiles in a military parade in Tehran on Monday, with the rockets sporting slogans including "Israel must be wiped off the map".
The United Nations nuclear watchdog, the International Atomic Energy Agency, has imposed an October 31 deadline on Iran to prove it is not secretly developing nuclear weapons and also urged it to suspend enriching uranium, which the United States claims could be used to make nuclear bombs.
Israeli Foreign Minister Silvan Shalom said late last month that Iran's pursuit of a nuclear capability is a "nightmare scenario" which demands immediate international action.
"Iran is fast approaching the point of no return in its efforts to acquire nuclear weapons capability," Shalom said.
"It's urgent that the international community act to ensure that this nightmare scenario is prevented."