An RAF jet carrying the defence secretary, John Healey, had its signal jammed for the entire three-hour flight after it flew near the Russian border.
Healey had been visiting British soldiers in Estonia and was travelling back to the UK when the electronic attack happened, the Times reported.
It is thought Russia was behind the incident on Thursday.
Smartphones and laptops were unable to connect to the internet and pilots had to use a different navigation system as the plane’s GPS was disabled.
It is unclear if Healey was deliberately targeted but the flight path was visible on aircraft tracking websites.
Passengers, who included photographers and a reporter, were told the Dassault Falcon 900LX aircraft could still operate safely.
Healey had met the Estonian minister of defence, Hanno Pevkur, in Tallinn to discuss long-term bilateral defence cooperation and its strategic expansion.
On Wednesday the Ministry of Defence (MoD) revealed two Russian jets had “repeatedly and dangerously” intercepted an RAF spy plane above the Black Sea last month.
A Russian Su-35 jet flew so close to the British reconnaissance aircraft that it triggered its emergency systems, including disabling the autopilot.
A Russian Su-27 also flew six metres from the unarmed Rivet Joint’s nose and carried out six passes in front.
The MoD said it was the most dangerous Russian action against a British Rivet Joint aircraft since a plane fired a missile over the Black Sea in 2022.
A Rivet Joint is a spy plane, with a crew of up to 30, capable of a wide range of electronic surveillance at a ranges of about 150 miles, and would have been monitoring Russian activity as part of a Nato patrol.
In March 2024, an RAF plane carrying the then-defence secretary Grant Shapps had its GPS signal jammed while flying near Russian territory.
The satellite signal was interfered with for about 30 minutes while the flight was heading back to the UK from Poland.
Last month, Healey revealed the UK had tracked three Russian submarines that loitered over critical undersea infrastructure in the North Atlantic for a month before they sailed away.
“I would like to pay tribute to the outstanding professionalism and bravery of the RAF crew who continued with their mission despite these dangerous actions,” he said.
“Let me be very clear: this incident will not deter the UK’s commitment to defend Nato, our allies and our interests from Russian aggression.”