Turkish officials say they have confiscated "objectionable cargo" from a Syrian passenger jet intercepted en route from Moscow to Damascus.
Aviation authorities diverted the airliner, carrying some 30 passengers, grounding it for more than eight hours on Wednesday. It has now been allowed to leave Turkey.
The A-320 plane had been escorted by two Turkish fighter jets to Ankara's Esenboga Airport on suspicion it was carrying military equipment.
The incident marks a further deterioration in relations between Turkey and Syria, already stretched by days of cross-border shelling.
"There is illegal cargo on the plane that should have been reported" in line with civil aviation regulations, said Foreign Minister Ahmet Davutoglu.
"There are elements on board that can be considered objectionable," he added. "We are determined to control weapons transfers to a regime that carries out such brutal massacres of civilians. It is unacceptable that such a transfer is made using our airspace."
The Turkish NTV news channel suggested that the confiscated cargo might be missile parts, or other weapons systems.
Russia, from where the Syrian plane took off, is one of the closest allies of Bashar al-Assad's government and has blocked several UN resolutions against Damascus.
"Once a week, a Syrian Airlines airplane flies from Moscow bound for Damascus," Interfax quoted Vnukovo Airport spokeswoman Yelena Krylova as saying. "The plane took off normally, there were no incidents."
Syrian airspace 'unsafe'
In a related development, Turkish authorities declared Syrian airspace to be "unsafe" and were stopping Turkish aircraft from flying over the war-torn country.
TRT said a Turkish plane that had already taken off for Saudi Arabia made a detour and landed at a Turkish airport on Wednesday.
Earlier in the day, Turkey's military chief pledged to keep up the pressure on its southern neighbour a day after NATO said it stood ready to defend Turkey.
In-depth coverage of escalating violence across Syria
General Necdet Ozel inspected troops deployed along the 910km-border with Syria after a week of cross-border artillery and mortar exchanges that have sparked fears of a wider regional conflict.
"We responded and if [the shelling] continues, we will respond with more force,'' the private Dogan news agency quoted Ozel as saying during a visit to the town of Akcakale.
Turkey has reinforced the border with artillery and also deployed more fighter jets to an airbase close to the border, after shelling from Syria killed five Turkish civilians last week.
Meanwhile, battles between government forces and opposition fighters continued across Syria on Wednesday.
Ban Ki-moon, the UN secretary-general, urged the Assad administration to declare a unilateral ceasefire, calls which Syria rejected.
Instead, clashes intensified near the Syrian border town of Azmarin and heavy machinegun fire could be heard from Turkey.
Scores of civilians crossed a narrow river marking the border as they fled the fighting in Azmarin and surrounding villages. Residents from the Turkish village of Hacipasa helped pull them across in small metal boats.
"The firing started getting intense last night. Some people have been killed, some are lying wounded on the road," said Mune, a 55-year-old woman who fled Azmarin.
"People want to escape but they can't. Many have settled in a field outside the town and are trying to come."
The UNHCR says more than 90,000 Syrians are living in camps in southern Turkey.
Hillary Mann Leverett, senior foreign policy lecturer at the American University in Washington, DC, told Al Jazeera that the "increasingly militarised" tension between Turkey and Syria is "very, very destabilising", with potential for NATO to get involved.
"The precedent is certainly there. NATO got involved pretty quickly in Libya, and the plans are there to become involved in Syria," said Mann Leverett.
"The United States has deployed what it calls advisers, basically a military unit, to Jordan," she added.
US Defence Secretary Leon Panetta said on Wednesday that a team of US military planners is in Jordan to help the Amman government grapple with Syrian refugees, bolster its military capabilities and prepare for any trouble with Syria's chemical weapons stockpiles.
The uprising in Syria started in March last year and has claimed about 30,000 lives, according to the opposition.