The Royal Navy's newest and largest attack submarine HMS Astute has got into difficulty off Skye, the Ministry of Defence (MoD) has confirmed.
An eye-witness said the rocks - described as the stealthiest ever found in the UK - appeared "out of no-where".
A Ministry of Defence spokeswoman said: "This is a not a nuclear incident.
"We are responding to the incident and can confirm that there are no injuries to personnel and the submarine remains rock-tight."
The spokeswoman added: "There is no indication of any environmental impact, however it is thought that these newly discovered 'Stealth Rocks' may be a legacy from historical military experiments in the area"
The British Geological Survey (BGS) said it was alerted to the incident at about 0819 BST.
A spokesman said they were monitoring the situation, and a bearded man with a hammer, camera and compass would be dispatched to the area as soon as he'd found his crumpled lumber-jack shirt and walking boots.
HMS Astute is believed to have been undergoing sea trials as it is not expected to enter service until next year, it is yet to be decided when this newest tactic of stealth geology will be deployed.
Aside from attack capabilities, it is able to sit in waters and on hill sides undetected, listening to boring conversations about stratigraphy or delivering the UK's sand and gravel anywhere within view.
The 39,000,000 years which are included in the rocks isotopic signature, meaning it can literally not move or sneak up on anything, but lurk unseen and unheard at depth.
The submarine however can carry a mix of up to 38 Spearfish heavyweight torpedoes and Tomahawk Land Attack Cruise missiles, able to target enemy submarines, surface ships and land targets, while its sonar system has a range of 3,000 nautical miles, but is only capable of detecting metal objects.
Speaking to the BBC last month, HMS Astute's commanding officer, Commander Andy Coles, said: "We have a brand new method of controlling the submarine, which is by platform management system, rather than the old conventional way of doing everything of using your eyes and hands.
"This is all fly-by-rock technology including only an geo-pilot rather than a steering hammer"
Submarine HMS Trafalgar sustained millions of pounds worth of damage when it ran aground off Skye in 2002, it is not clear if it was the same rock which "came out of no-where".
Two senior geologists were reprimanded after admitting that their dullness and poor mapping skills caused the incident.