"We will use all strike weapons at our disposal and the Shahab-3 missile is one of those," Shamkhani told reporters on Wednesday after a cabinet meeting.
He was replying to a query about whether Tehran would retaliate with missiles if Israel made good its threats to take out Iranian nuclear sites.
Earlier this year, the air force of the Islamic Revolutionary Guards Corps took delivery of several domestically built Shahab-3 missiles, with a range of between 1,300 and 1,500 km, sufficient to reach Israel.
The Tel Aviv daily Haaretz on Sunday quoted Israeli Defence Minister Shaul Mofaz as warning that the Jewish state was considering striking the nuclear facilities of Iran.
Israel now regards Iran its arch foe, despite an agreement earlier this month to submit them to snap UN inspections.
If such attacks are launched, "the necessary steps will be taken so that Iranian citizens will not be harmed," the daily quoted Mofaz as saying.
"The remarks by the Israeli war minister Mofaz show that the Zionist regime is a pariah regime"
Defence Minister, Iran
The Iranian defence minister said: "Israel is a glass garrison, but the Zionist regime leaders think that this garrison should have sovereignty over the whole world."
"The remarks by the Israeli war minister Mofaz show that the Zionist regime is a pariah regime," said Shamkhani.
"The Israeli threats will not have any effect on the decisions of Iran. If threats against Iran are to be carried out, the Islamic Republic of Iran will answer with all its forces", he said.
On Monday, the head of the Iranian air force, Brigadier General Seyed Reza Pardis, warned that Israel will "dig its own grave" if it attacks Iranian nuclear sites.
"The threats of the Zionist regime hold no value for us," he said, adding: "The (Zionist) regime knows that the armed forces of the Islamic republic, in particular our air force, have such high capabilities ... that it would be digging its own grave in the region if it launches military attacks against Iran."
Iran last week won plaudits from the international community by signing the additional protocol of the nuclear Non-Proliferation Treaty that opens the way for snap UN inspections of sites.
Iran says Israel should now follow its lead and bring its own nuclear facilities under international supervision.