Once close allies, the two countries' relationship quickly deteriorated as President Bashar al-Assad intensified a crackdown in a 17-month-old uprising against his rule.
Several military officers have defected to Turkey and the nominal commander of the Free Syrian Army, a loosely coordinated group of insurgents fighting Assad's forces, is also based there.
"The Turkish government plays a fundamental role in supporting terrorism by opening its airport and borders to host al Qaeda elements, jihadists and salafists," Syria's foreign ministry said in a statement circulated on state television.
"The Turkish government has set up on its soil military offices where Israeli, American, Qatari and Saudi intelligence agencies direct the terrorists in their war on the Syrian people," the statement said.
Damascus also accused France and the United States of sending opposition fighters communications equipment. US sources have said President Barack Obama signed a secret order authorizing US support for opposition fighters seeking to depose Assad.
Gulf sources told Reuters that Turkey had set up a secret base with allies Saudi Arabia and Qatar to direct vital military and communications aid to Syria's opposition fighters from the city of Adana near the border.
The statement said Turkey had used the camps as "military bases" for terrorists who then headed to Syria to commit crimes.
A Turkish foreign ministry spokesman said: "It is not the first unsupported claim coming from Syria. These speculative claims are not reflecting the truth."