The Russian fighter plane “exited Turkish airspace into Syria” after being intercepted, the ministry said.
The Turkish minister has spoken to his Russian counterpart, as well as ministers from other NATO countries.
Russia has been carrying out air strikes in Syria in support of President Bashar al-Assad.
The Russian embassy in Ankara said a Russian plane did violate Turkish airspace, and Russia has “explained it” to Turkey, Interfax reports.
However, a Kremlin spokesman in Moscow did not confirm the incident: “Our ambassador was called to the foreign ministry and given a note, which mentions certain facts, which will be checked.”
The Russian air campaign began on September 30 with Moscow insisting it was targeting ISIS positions.
However, Syrian activists say Russian planes have also targeted other Syrian groups opposed to President Bashar al-Assad.
On October 5, Russia said it had “continued performing pinpoint strikes” on ISIS targets in Syria, carrying out 25 sorties and hitting nine ISIS targets.
Among those targets was a communications centre in Homs, and a command centre in Latakia, it said.
NATO said its Secretary-General Jens Stoltenberg would meet the Turkish Foreign Minister Feridun Sinirlioglu at the organization’s headquarters in Brussels on October 5.
Last week Turkish President Recep Tayyip Erdogan described the Russian intervention in Syria as a grave mistake that would further isolate Moscow.
Saturday’s interception took place south of the Yayladagi/Hatay region, Turkey says.
The foreign ministry in Ankara summoned the Russian ambassador to issue a “strong protest” against the incident, it said.
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