The 70,000-tonne HMS Queen Elizabeth - the largest warship in the Royal Navy - was docked in Invergordon in the Highlands when the drone was flown close to the carrier last month.
The tiny aircraft then landed itself on the deck of the £3 billion vessel after sensing a high wind risk.
The anonymous photographer - a member of the Black Isle Images amateur photography group - said he was surprised to have been unchallenged, even when he reported the incident to armed guards at the dock.
The drone pilot told BBC Scotland: “I could have carried two kilos of Semtex and left it on the deck.
“I could have been anybody. It was like a ghost ship.”
The photographer took the oppportunity to take footage of the new aircraft carrier when it arrived in Invergordon last month, piloting his DJI Phantom drone from the other side of the Cromarty Firth.
The drone was equiped with anti-crash sensors which automatically land the aircraft if it is in danger.
The non-slip coating of the carrier’s deck allowed the drone - which usually avoids steel structures - to touch down. The drone pilot then took a photograph and managed to take off again.
A spokesman for the Ministry of Defence said: ‘We take the security of HMS Queen Elizabeth very seriously.
“This incident has been reported to Police Scotland, an investigation is under way and we stepped up our security measures in light of it.”