The Foreign Ministry said the Turkish action violated international law and showed Ankara's "hostile policy" towards Syria.
"All contents of the civilian Syrian plane that Turkish authorities forced to land at Ankara airport were listed on the statutory bill of lading and on the plane's manifest. It was not carrying any kind of weapons or prohibited goods," the ministry said in a statement.
The head of Syrian Arab Airlines, Ghaida Abdulatif, said the cargo consisted of civilian packages with electrical equipment which had been officially registered.
The state news agency SANA also quoted Abdulatif as saying Turkish authorities "assaulted the plane's crew before it was allowed to take off", without giving details.
Lebanon's al-Manar Television earlier quoted Syria's transport minister as describing Turkey's action as an act of air piracy.
Turkish officials suspected it was carrying military equipment to Syria, where President Bashar al-Assad's forces are fighting rebels.
The Foreign Ministry said that by using military means to force the plane to land, the Turkish government violated international laws.
"The sudden appearance of military aircraft, without justification or warning, threatened the safety of the plane and passengers," it said.
"This hostile and deplorable Turkish act is an additional indication of the hostile policy of Erdogan's government, considering that it trains and harbours terrorists and helps them infiltrate into and bombard Syrian territory."
Turkey, once an ally of Assad, has become a leading international voice calling for him to quit and has allowed rebel leaders sanctuary on its territory.
The cargo incident adds to increased tensions as the two sides square off against each other along their border after Syrian artillery fire landed on Turkish soil last week.
The Syrian Foreign Ministry statement added a conciliatory note, saying that despite the Turkish government's aggressive behaviour, Syria still wanted to maintain friendly relations with the Turkish people.
Airlines chief Abdulatif said Turkey's action was "inhumane" and that the airline would lodge a complaint with international aviation authorities. (Reuters)