"I can confirm that we have detected the launch of Scud-type missiles; we strongly regret that act," Rasmussen said, adding: "I consider it an act of a desperate regime approaching collapse."
The latest launches were detected on Thursday, a source close to NATO said.
The use of such missiles by President Basahar al-Assad's regime also highlights the "need for effective defence and protection of our ally Turkey," Rasmussen said, referring to the planned deployment of Patriot anti-missile batteries along its southern border with Syria.
Rasmussen stressed that the missiles had not landed on Turkish territory but they nonetheless posed a potential threat which had to be countered.
The Patriot deployment, to be made by NATO allies the United States, Germany and the Netherlands, is for a "defensive purpose only," he said.
The mobile medium-range Scud, is a Soviet-era missile which can carry a warhead of up to 1,000 kilograms (2,200 pounds). The missiles can be equipped with conventional, chemical or nuclear warheads.