Tehran has previously made clear its displeasure at Turkey's agreement to deploy an early warning system for missiles, part of the NATO shield structure, on its soil.
Iranian officials have said the plan will be used as an "eye" for Israel by giving it greater surveillance over countries in the region.
The shield is intended primarily to counter perceived threats from Iran and North Korea, although Turkish officials have said the system is not aimed at any specific country.
The claim by the Hajizadeh, which he did not back with any scientific data, is the latest in a series of warnings Tehran has issued against the plan.
Hajizadeh warned last year that his country could target the relevant installations in Turkey if faced with a military attack.
"We have prepared ourselves if any threat is staged against Iran," he was quoted as saying last November. "We will target NATO's missile shield in Turkey and will then attack other targets."
Iran’s Foreign Minister Ali Akbar Salehi, however, dismissed the threats and reassured Turkey that they are not Iran's official policy, according to reports by Turkish media.
Iran and Turkey have also been at odds over Tehran’s main regional ally, Syria.
Ankara has been vocal in the international condemnation of the government crackdown in Syria, while Iran appears to be determined to continue supporting the Bashar al-Assad government.
Earlier this month Iranian officials sharply criticized Turkey for hosting a conference on the Syrian crisis.
Despite the recent tensions, Turkey has also played an important role as a facilitator for nuclear talks between Iran and major world powers.
-- Golnaz Esfandiari