Turkish Foreign Minister Ahmet Davutoglu told state-run television that Ankara had received information that the plane could be carrying "non-civilian cargo".
The aircraft was escorted by two Turkish jets to the capital's Esenboga airport for security checks.
Local media reports say military communication devices were seized by the Turkish authorities for further examination and the aircraft was later granted permission to leave.
"We are determined to control weapons transfers to a regime that carries out such brutal massacres against civilians. It is unacceptable that such a transfer is made using our airspace," Mr Davutoglu said in comments broadcast live on state television.
"Today we received information this plane was carrying cargo of a nature that could not possibly be in compliance with the rules of civil aviation," he said.
Meanwhile, the Turkish authorities have declared Syrian airspace to be unsafe and are preventing Turkish aircraft from flying over the country.
The BBC's James Reynolds in southern Turkey says Ankara clearly wants to show its own population and Syria that it is taking the threat posed by Syria extremely seriously.
