On Tuesday, Flight-tracking website Flightradar reported that a number of Russian domestic flights destined for St Petersburg had been returned to their departure points.
Russia's Defense Ministry later said it had conducted air exercises using previously unannounced interceptor aircraft, which had caused the flights to be canceled.
At least five flights from Moscow to Russia's second-largest city were diverted to the capital as of 11 a.m. local time (0800 UTC/GMT), after initially going airborne.
Traffic resumed soon after, amid unconfirmed Russian media reports that an unidentified object such as a drone had been spotted in the area.
A Russian online news website, Baza, stated that fighter jets were sent to investigate after the unidentified object was spotted in the sky. Later reports said the planes had not found anything.
News agencies reported later on Tuesday that flights had started again and that a temporary airspace ban within a radius of 200 kilometers (124 miles) from Pulkovo Airport had been lifted by noon local time.
In a statement issued about an hour after the resumption of flights, the Defense Ministry said it was conducting exercises that included sending fighter jets into Russia's western airspace.
"During the training, air defense forces worked on the detection, interception, and identification of targets, as well as interacting with emergency services and law enforcement agencies," Russian news agencies cited the ministry as saying.
Pulkovo, about 15 km (about 9 miles) south of central Saint Petersburg, is the fourth busiest airport in Russia. The airspace closure was also said to have affected flights en route to and from the Russian exclave in Kaliningrad.