"We can indeed confirm that there was GPS jamming, but the plane landed safely in Bulgaria. We have received information from the Bulgarian authorities that they suspect that this was due to blatant interference by Russia," the spokesperson said on Monday.
The Russian government did not immediately reply to a request for comment.
The EU gave no further details, but the spokesperson said the incident on Sunday would reinforce the bloc's "unshakable commitment to ramp up defence capabilities and support for Ukraine" against Russia's three-and-a-half-year-old invasion.
It did not address the question of whether the EU believed von der Leyen's airplane had been deliberately targeted.
In a statement, Bulgaria's government said the GPS signal was lost as von der Leyen's plane approached the southern city of Plovdiv, prompting air traffic controllers to switch to ground-based navigation systems to ensure a safe landing.
It said von der Leyen had been travelling on a plane chartered by the European Commission.
Last year Estonia accused Russia of jamming GPS navigation devices in airspace above the Baltic states. Finnair had to divert two flights back to Helsinki after GPS interference prevented their approach to Tartu in eastern Estonia.
EU Defence Commissioner Andrius Kubilius said on Monday the 27-nation bloc would increase its number of satellites in low orbit to enhance detection of interference.
GPS jamming uses a frequency transmitting device to block or interfere with radio communications, usually by broadcasting signals from the ground that are stronger than satellite-based signals.
When a system is jammed, it might have to be switched off for the duration of the flight, which can cause stress and delays for take-off and landing because certain procedures require GPS to function.
But major airports have a variety of navigation tools available if GPS isn't working.
The incident with von der Leyen's plane occurred while she was on a four-day tour of EU member states that border Russia, Belarus or the Black Sea.
"There she has seen first-hand the everyday challenges of threats coming from Russia and its proxies," the Commission spokesperson said.
"The EU will continue to invest in defence spending and in Europe's readiness even more after this incident."
