The government says Russian planes carrying out airstrikes in Syria crossed into Turkish territory over the southern province of Hatay for a second time.
NATO has warned of the "extreme danger" of such violations and condemned the incursions.
Turkey launched fighter jets after Russian planes twice entered Turkish air space.
Turkey's government calls it an "unacceptable" intrusion.
But it's a simple mistake, according to Russian Defence Ministry spokesman Igor Konashenkov. "The incident occurred because of unfavourable weather conditions in that area. You shouldn't be looking for any conspiratorial reasons in this case."
Ahmet Davutoglu, the Turkish Prime Minister, was diplomatic in response but his implication was clear. "Whoever it is, wherever it comes from, whatever direction it comes from, our rules of engagement are clear when our airspace is violated."
Russian planes could be shot down if the "mistake" is repeated.
The incident prompted an emergency meeting of NATO leaders and a warning from Jens Stoltenberg, NATO Secretary General, of the extreme danger of such behaviour.
"Russia's actions are not contributing to the security and stability of the region. I call on Russia to fully respect NATO airspace and to avoid escalating tensions with the alliance."
NATO also wants Russia to stop attacking Syrian opposition fighters and civilians.
The Russian government says its mission aims to weaken IS militants.
But Turkey and most Western powers see it as support for President Bashar Al-Assad.
White House spokesman Josh Earnest says that's borne out by the targets being attacked by the Russians. "They are actually concentrating their efforts on territory held by opponents of the regime, which may include some extremists, but don't, according to our analysts, include many, if any, ISIL forces."
Russia has suggested cooperating with the US on bombing missions.
US Secretary of State John Kerry warns that without it, the risk of a serious confrontation is high. "It is precisely the kind of thing that, had Turkey responded under its rights it could have resulted in a shootdown, and it is precisely the kind of thing we warned against."
Turkey's threat to respond if provoked again raises the prospect of direct confrontation between the former Cold War enemies.
