"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.
"Now is the time for Iran to send these clear messages to the Syrian regime," he said.
"Today if there is an element in the region that threatens peace, it is the Syrian regime's aggressive policies."
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 military 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.
"What we expect from Iran is not to make statements on the deployment of a defensive system but to use its leverage and give very clear messages in order to make sure that the oppression stops," Davutoglu said.
Turkey has turned to its NATO allies for the deployment of Patriot missiles along its border after a series of cross-border shellings including the one in October which killed five Turks.
NATO chief Anders Fogh Rasmussen on Monday denounced claims by the head of Iran's armed forces and said: "We are there to defend and protect Turkey. We have no offensive intention whatsoever."
Turkey also insists the system is purely defensive.
"Those who closely follow the issue are aware that the Patriot system is for defence and will not operate unless there is any attack (targeting Turkey)," Davutoglu said.
But both Russia and Iran, the most powerful allies of the Assad regime, are opposed to the move, fearing it could spark broader conflict.
Germany, the Netherlands and the United States have agreed to provide the missile batteries, which would come under NATO command.
On Tuesday, around 40 German officers were surveying possible sites in Turkey's southeast for the deployment.
Relations between Iran, Syrian President Bashar al-Assad's main regional ally, and Turkey, a fierce critic of the Damascus regime, have been strained over the 21-month conflict in Syria.
Some Iranian officials have accused Turkey of arming Syrian rebels, charges repeatedly rejected by Ankara.
Iranian President Mahmoud Ahmadinejad cancelled a planned Monday visit to Turkey "because of a busy schedule", his office said amid tensions with Ankara over the deployment of Patriots. He was to have met with Turkish Prime Minister Recep Tayyip Erdogan.
Iran has detailed a six-point plan to put an end to the crisis in Syria, calling for an immediate ceasefire and the start of national dialogue between Damascus and rebel forces.
However opposition groups reject any Iranian involvement in the search for a solution, reflecting the view that the US and some Western and Arab countries hold that Tehran is discredited by its unwavering support for Assad.
And Turkey, which pioneered a regional mechanism involving Tehran and Egypt to end the Syrian conflict, backs Tehran's plan as long as it leads to a solution.
"Turkey backs every initiative which will help stop the bloodshed in Syria and welcomes every effort in this regard," a Turkish foreign ministry diplomat told AFP, when asked about the Iranian plan.