The S7 carrier said the crew of the A-319 Airbus jetliner, en route to the Siberian city of Novosibirsk, received a warning from air traffic controllers in Mongolia that it would not be permitted into the country's airspace, and had to return to its departure point.
The ban was lifted some time later, when the plane was already on its way back to the Chinese capital.
"Such incomprehensible and inconsistent actions by our Mongolian counterparts are very bewildering indeed," S7 spokesman Yevgeny Filyanin said. "I think there will be an inquiry [into the incident]."
He said the Mongolian side gave no explanation as to why it had denied entry to the Russian plane without any prior notice.
According to S7, the plane is currently in Beijing preparing for a repeat flight to Novosibirsk.