"We will improve the Shahab-3 and when we test it, in the very short future, we will let you know," what improvements have been made, said the minister, who was quoted by the student news agency ISNA.
"These improvements do not only concern its range, but other specifications as well," Shamkhani said, without giving more details.
Israel late last month successfully tested its Arrow II anti-missile missile in the United States. It was the seventh time the missile has worked, but the first time it destroyed a real Scud missile.
Israeli officials made it clear the improved anti-missile system was aimed squarely at fending off any attack by Iran, Israel's arch foe.
Shamkhani insisted the Shahab-3 was intended for defensive purposes.
Tehran fears Israel could strike its controversial nuclear program, which Washington suspects is being used to covertly develop weapons.
"The Israelis are trying hard to improve the capacity of their missiles, and we are also trying to improve the Shahab-3 in a short time," he said, denying the Islamic republic was working on a more advanced Shahab-4.
Tehran finalised its testing of the Shahab-3 only in June.
The missile, whose name means "meteor" or "shooting star" in Farsi, is thought to be capable of carrying a 1,000 kilogramme (one-ton) warhead at least 1,300 kilometers (800 miles), well within range of Israel.
Six Shahab-3 missiles were paraded in Tehran in September during commemorations of the 1980-88 Iran-Iraq war. One of them carried a banner declaring "We will wipe Israel from the map".
The Shahab-3 is believed to be derived from technology acquired from Pakistan and North Korea, though Shamkhani denied any dealings between Tehran and Pyongyang.
When asked if the army was involved in Iran's nuclear program, Shamkhani said that its "only intervention in the nuclear area, is nuclear protection," referring to possible attack from Israel's suspected nuclear arsenal.
"If a military operation is carried out against us, we cannot do nothing, so we are investing in nuclear protection," he said.