The navigation system of a plane carrying Ursula von der Leyen was disrupted due to suspected Russian interference, the European Commission said.
A spokesperson said the "GPS jamming" happened while the Commission president was about to arrive in southern Bulgaria on Sunday, but she still landed safely.
They added: "We have received information from the Bulgarian authorities that they suspect that this was due to blatant interference by Russia."
The Financial Times, citing unnamed officials, reported that von der Leyen's plane had to land at Plovdiv Airport with the pilots using paper maps.
The European Commission said "threats and intimidation are a regular component of Russia's hostile actions" and that the incident would reinforce its commitment to "ramp up our defence capabilities and support for Ukraine".
The Bulgarian government confirmed that, during the flight, "the satellite signal transmitting information to the plane's GPS navigation system was neutralised".
The statement continued: "To ensure the flight's safety, air control services immediately offered an alternative landing method using terrestrial navigation tools."
Kremlin spokesperson Dmitry Peskov told the FT that its information was "incorrect".
Bulgaria's Air Traffic Services Authority told the paper that there had been a "notable increase" in navigation jamming since January 2022.
Experts have have previously warned that Russia was causing disruption to satellite navigation systems - affecting thousands of civilian flights.
Cyrille Rosay, a senior cybersecurity expert at the European Union Aviation Safety Agency (EASA), told the BBC that such cases had worsened since Russia's full-scale invasion of Ukraine.
Moscow has regularly denied scrambling the satellite-based systems, which are used to determine a plane's location.
Von der Leyen was visiting Bulgaria as part of a tour of eastern EU states to discuss defence readiness.
A Commission spokesperson said she had "seen first hand the every day threats from Russia and its proxies" during the tour.
