"Instead of criticising the (Patriot missile) system, Iran should say stop to the Syrian regime that has been continuously oppressing its own people and provoking Turkey through border violations," Davutoglu told reporters in Ankara.
"It is time to send clear messages to the Syrian regime."
His comments came after Iranian political and military officials voiced concerns about NATO's decision to deploy US-made Patriot missiles along the volatile Syrian-Turkish border in case of an attack emanating from Syria.
Iran's armed forces chief of staff on Saturday warned Turkey over its plans to deploy the missiles, saying the move was part of a Western plot to "create a world war". Iranian Foreign Minister Ali Akbar Salehi called the planned deployment "provocative" and said it could bring about "uncalculated" results.