Turkey asked NATO for the Patriot system, designed to intercept aircraft or missiles, last week after talks about how to shore up security on its 900-km (560-mile) border.
"The installation of such systems in the region has negative effects and will intensify problems in the region," Iranian parliament speaker Ali Larijani said on returning from a trip to Syria, Lebanon and Turkey on Saturday evening, according to Iranian state news agency IRNA.
Ramin Mehmanparast, Iran's foreign ministry spokesman, told the Iranian Students' News Agency (ISNA) on Sunday that deploying the Patriot system "will not only not help solve the situation in Syria, it will actually make the situation more difficult and complicated as well".
Syria has called Turkey's request for the Patriot missiles "provocative", and Russia said the move could increase risks in the conflict.
Iran has steadfastly supported Syrian President Bashar al-Assad throughout the 20-month-old uprising against his rule.
Turkey's missile request may have riled Damascus because it could be seen as a first step toward implementing a no-fly zone over Syrian airspace.
Syrian rebels have been requesting a no-fly zone to help them hold territory against a government with overwhelming firepower from the air, but most foreign governments are reluctant to get sucked into the conflict.
Turkey fears security on its border may crumble as the Syrian army fights harder against the rebels, some of whom have enjoyed sanctuary in Turkey.
Heavy fighting has often erupted along Syria's border with Turkey. Ankara has scrambled fighter jets and returned fire after stray Syrian shells and mortar bombs landed in its territory.
Turkish Foreign Minister Ahmet Davutoglu said on Sunday no one should be concerned by the use of Patriots.
"These systems are solely defensive mechanisms, and will not become active unless there is a direct threat to our country's security," Davutoglu said, speaking to CNN Turk.
"The aim of this action is to protect Turkey's borders as much as possible at a time of crisis. The Patriots will be sent back when the risks to Turkey's security disappear."
(Reporting by Yeganeh Torbati in Dubai, additional reporting by Ece Toksabay in Istanbul; editing by Andrew Roche)