Turkish F-16 fighter jets were scrambled after a Russian warplane violated Turkey's air space on Saturday, the foreign ministry said.
Russia said the incident was a "navigational error" and that it has "clarified" the matter to Ankara.
Turkish jets patrolling the border were also "harassed" by an unidentified plane on Sunday, Turkey said.
Russia has been carrying out air strikes in Syria in support of President Bashar al-Assad.
Turkey, a Nato member, has called the Russian strikes a "grave mistake".
Representatives of Nato's 28 member states will meet later to discuss the incursion into Turkey.
On Monday, Russia said it had "continued performing pinpoint strikes" on IS targets in Syria, carrying out 25 sorties and hitting nine Islamic State (IS) targets.
Among those targets was a communications centre in Homs, and a command centre in Latakia, it said.
The Russian air campaign began on Wednesday, with Moscow saying it was targeting IS positions and those of other extremists.
But Turkey and other members of the US-led coalition in Syria say the principal target is in fact the Syrian opposition groups fighting President Assad.
They assert that Russia's intervention will further escalate the conflict and risks driving more recruits to IS.
Saturday's interception took place near Yayladagi in its southern Hatay region, Turkey says. The foreign ministry in Ankara said it had summoned the Russian ambassador to issue a "strong protest".
Turkish Prime Minister Ahmet Davutoglu told Turkish TV that the rules of engagement were clear, whoever violates its airspace.
"The Turkish Armed Forces are clearly instructed. Even if it is a flying bird, it will be intercepted," he said.
But he played down the possibility of a "Turkey-Russia crisis", saying that channels between the two countries remained open.
"Russia respects Turkey's borders and will not let this happen again," he said.
The Turkish foreign minister, Feridun Sinirlioglu, has spoken to his Russian counterpart Sergei Lavrov, as well as ministers from other Nato countries.
The Russian fighter plane "exited Turkish airspace into Syria" after being intercepted, the ministry said.
After meeting the Turkish Foreign Minister in Brussels, Nato Secretary General Jens Stoltenberg said the incursion was "unacceptable".
"Russia's actions are not contributing to the security and stability of the region," he said.
The UK ambassador to Turkey described the incursion as "reckless and worrying" and said Nato allies stood "shoulder to shoulder" with Turkey.