Turkish President Recep Tayyip Erdogan warned Moscow that it would lose a lot if it destroyed its friendship with Ankara, adding that his country would not remain patient in the face of violations of its air space by Russian warplanes.
Turkey on Thursday said it summoned the Russian ambassador to Ankara for a second time after a new incursion by a Russian fighter jet on Sunday.
"Our positive relationship with Russia is known. But if Russia loses a friend like Turkey, with whom it has been cooperating on many issues, it will lose a lot, and it should know that," Erdogan said.
Russia's embassy in Ankara said it was looking into the fresh allegation.
The first reported violation of Turkish airspace took place on Saturday, prompting a sharp warning from Turkey that future violations could lead to an implementation of the rules of engagement and condemnation from NATO.
Turkey is a member of the alliance.
Has Russia saved the Assad regime from collapse?
The Russian embassy confirmed that "such an incident took place", according to the Interfax news agency.
Russia last week began bombing what it says are Islamic State in Iraq and the Levant (ISIL) group targets in the Syria, though the air strikes seem to be largely hitting different opposition groups fighting President Bashar al-Assad.
The strikes seem to be focused on frontline areas where Assad's forces are facing losses to the rebel factions, especially in the provinces of Idlib and Hama in the north.
These areas have no ISIL presence.
Russia is a firm backer of Assad, while Western nations and Turkey say Assad has lost the legitimacy to continue in power over the longer term.
Russia has also been accused by Western officials and activists on the ground that many of the targets since the beginning of its campaign on Wednesday were civilian.
Russia denies the claim.
Strikes in Palmyra
On Tuesday, Russian jets hit ISIL targets in the Syrian city of Palmyra and the northern province of Aleppo, Syrian state television and a monitoring group said.
The strikes destroyed 20 vehicles and three weapons depots in ISL-held Palmyra, state television said, quoting a military source.
Palmyra's Roman-era ruins under the ISIL control
In Aleppo, they hit the towns of Al-Bab and Deir Hafer, about 20 km east of a military airport currently besieged by Islamic State fighters.
The Syrian Observatory for Human Rights, a Britain-based group tracking Syria's conflict, said the Palmyra strikes killed 15 ISIL fighters.
ISIL forces captured Palmyra in May, an advance which brought them closer to the core of government-held territory in western Syria. It also put the city's Roman-era ruins under the their control.
Syria's antiquities chief Maamoun Abdulkarim said on Sunday Islamic State fighters blew up Palmyra's Arch of Triumph , one of the most treasured monuments in the 2,000-year-old city. They had already destroyed temples and other antiquities.
Source: Al Jazeera and agencies