But officers insisted the ship was fully defended against any such breaches and would have its own team of cyber security specialists once fully operational.
Commander Mark Deller, commander air of the ship, told the Guardian: “The ship is well designed and there has been a very, very stringent procurement train that has ensured we are less susceptible to cyber than most.
“With regards to someone wanting to jam my radio frequencies, we will have an escort and destroyers around us that will ward off people who try and impact our output.
“That’s normal routine business at sea.”
And he said any out-of-date systems would get an upgrade. 'When you buy a ship, you don't buy it today, you bought it 20 years ago,” he explained.
Cyber warfare experts are set to join the carrier when it becomes operational in 2020.
Just before midnight on Monday, the 65,000 tonne vessel made its way beneath the world-famous Scottish bridge.
Crowds lined the river to see the carrier, described as the largest and most powerful ever built for the Royal Navy.
The huge vessel, which is set to be the nation's future flagship, and her 700-strong ship's company were heading to the North Sea for maiden sea trials over the summer.Earlier, naval staff and contractors lined the deck as the 280-metre carrier moved from Rosyth out into the Firth of Forth in a three-hour operation.
On Monday, Defence Secretary Sir Michael Fallon praised the voyage a “historic moment” for the UK.
"This floating fortress is by far the most powerful ship ever built in Britain that will enable us to tackle multiple and changing threats across the globe,” he said.
"HMS Queen Elizabeth is an enduring example of British imagination, ingenuity and invention that will help keep us safe for decades to come. She is built by the best, crewed by the best and will deliver for Britain.
"For the next 50 years she will deploy around the world, demonstrating British power and our commitment to confronting the emerging challenges from a dangerous world.
"The whole country can be proud of this national achievement."
The second ship in the class, HMS Prince of Wales, is being fitted out in the Rosyth dock and staff were able to look on as its sister ship set sail for the first time.