The Defence Secretary was returning from a visit to Poland where he watched hundreds of troops taking part in the biggest Nato exercise since the Cold War.
His aircraft's GPS signal and internet connection were "jammed" for around 30 minutes as it flew on the fringes of Kaliningrad on Wednesday.
Mr Shapps, who was travelling with his team and a group of journalists, was assured that the alleged electronic attack did not threaten the safety of the aircraft.
A defence source said: "While the RAF are well prepared to deal with this, it still puts an unnecessary risk on civilian aircraft and could potentially endanger people's lives. There is no excuse for this and it's widely irresponsible on Russia's part."
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