"The statements of the defence minister have not been reported accurately -- to some extent they have been altered," foreign ministry spokesman Hamid Reze Asefi was quoted as saying by the state news agency IRNA.
"We will not sit (with arms folded) to wait for what others will do to us," Shamkhani told Al-Jazeera TV on Wednesday when asked if Iran would respond to a US attack on its nuclear facilities, speaking in Farsi through an interpreter into Arabic.
"Some military commanders in Iran are convinced that preventive operations which the Americans talk about are not their monopoly," he added, according to the translator.
"America is not the only one present in the region. We are also present, from Khost to Kandahar in Afghanistan; we are present in the Gulf and we can be present in Iraq."
But Asefi said there had been "misinterpretations", adding, "Mr Shamkhani said that we would defend our territory and national interests and would allow no one to attack the Islamic republic.
"If anyone attacks our country, we will respond with determination."
Shamkhani's remarks were seen as an extension of an exchange of threats between Israel and Iran in recent weeks focussing on Iran's nuclear programme.
Iran insists that the programme, centred on the construction of a nuclear power plant at Bushehr, is purely peaceful but the United States and Israel in particular fear it conceals efforts to develop atomic weapons.
Speculation has arisen that Israel may strike at Bushehr, in a repeat of its attack against Iraqi nuclear facilities at Osirak in 1981.
Shamkhani added: "We will consider any strike against our nuclear installations as an attack on Iran as a whole, and we will retaliate with all our strength.
"Where Israel is concerned, we have no doubt that it is an evil entity, and it will not be able to launch any military operation without an American green light. You cannot separate the two."
"The US military presence (in Iraq) will not become an element of strength (for Washington) at our expense. The opposite is true, because their forces would turn into a hostage" in Iranian hands in the event of an attack, he said.
Earlier in the week, a commander of Iran's elite Revolutionary Guards was quoted as saying that Tehran would strike the Israeli reactor at Dimona if Israel attacks the Islamic republic's own burgeoning nuclear facilities.
The United States on Thursday reassured Tehran that US troops in Iraq pose no threat to Iran and that Washington will use diplomacy to address its concerns over Iran's nuclear program.
US State Department spokesman Adam Ereli said Iran's concerns that it was threatened by the troops were "unwarranted", and sought to appease what he called Tehran's "rhetoric concerning strikes and counterstrikes over Iran's nuclear program."
"From the United States point of view, this is a program that is of serious concern and it is something that we are committed to pursuing through diplomatic means, as evidenced by our active diplomacy through the International Atomic Energy Agency," Ereli said.