Turkish officials have accused a Syrian passenger plane of carrying “illegal cargo” between Moscow and Damascus.
Turkey intercepted the Syrian Air plane and searched it because of suspicions it was carrying military equipment.
But officials in Russia and Syria strongly denied the allegations and accused the Turkish authorities of endangering passengers and crew.
Tension between Turkey and Syria has been high since five Turkish civilians were killed last week by mortar bombs.
In response, Turkey fired into Syria for the first time since the uprising against President Bashar al-Assad began last year.
Turkey’s Foreign Minister Ahmet Davutoglu said “objectionable” cargo had been confiscated from the plane.
“There is illegal cargo on the plane that should have been reported,” he told the Anatolia news agency.
He did not specify whether any weapons had been found, but unconfirmed reports in Turkish media said the seized items included boxes of military communication equipment.
The foreign minister said Turkey, which imposed an arms embargo on Syria last year, would continue to investigate Syrian passenger planes flying over its air space.
Both Syria and Russia reacted angrily to the plane’s enforced diversion.
Syrian Transport Minister Mahmoud Saeed accused Turkey of carrying out “air piracy” and breaking civil aviation agreements, according to Lebanon’s al-Manar TV.
Gaida Abdul Latif, boss of Syrian Air, accused Turkey of endangering her passengers and crew.
“Turkish military aircraft forced the plane to land without giving prior warning to the pilot. The military aircraft were so close that there could have been an accident,” she said.
Russian Foreign Ministry spokesman Alexander Lukashevich said Turkish officials had failed to inform the embassy that 17 Russian citizens were on board the plane.
“We are concerned that, in this emergency situation, the lives and safety of the passengers, including 17 Russian nationals, were put at risk,” he said.
Russia’s state arms supplier Rosoboronexport said in a statement it had no information about the plane’s cargo, and denied it had any connection with the flight or anything on board.
Earlier, Mr Davutoglu had said Ankara was determined to stop any transfer of weapons to Syria through its airspace.
He said Ankara had received information that the Damascus-bound plane could be carrying “non-civilian cargo”.
The Airbus A320 airliner had about 30 passengers on board, far fewer than its 180 passenger capacity.
The aircraft was escorted by two Turkish fighters to the capital’s Esenboga airport for security checks.
It was allowed to take off at 02:30 (23:30 GMT on Wednesday), after several hours on the ground.
One passenger, Fatima el-Saman, told Turkish newspaper Hurriyet that there were no weapons on the plane.
“They were spare parts exported to Syria by a Russian businessman, as far as I could see,” she said.
In another sign of deteriorating relations, Turkish officials revealed on Thursday that Syria had stopped buying electricity from its neighbour last week.