"The whales had little food in their stomachs which suggests they were close to the shore and therefore not feeding.
"One possible explanation is that they were spooked by something further out to sea. This could include underwater noise such as an earthquake or an explosion."
Sarah Dolman, from the Whale and Dolphin Conservation Society's head of police for Scotland, said there is a strong possibility the explosions caused the whales to come dangerously close to shore.
She said: "That's why the post-mortem examinations that have taken place are vital. They show that there is no obvious reason why they came ashore.
"Pilot whales do occasionally strand in groups like this when one of the adults is sick or there has been a navigational error."
The Royal Navy confirmed a team of divers at the Cape Wrath bombing range in Scotland blew up two unexploded bombs last week left behind after an RAF training exercise.
One bomb was 540lb in size and the other 250lb.
The Royal navy conducts searches of the seabed around the Cape Wrath bombing range, which is used by all three armed forces, twice-a-year to dispose of any unexploded bombs.
A Royal Navy spokesman said: "From our point of view, to say that this is what caused the pilot whales to beach is sheer speculation. We have been operating in that area for years now."
Highland Council is working with the Scottish Environment Protection Agency and a local landowner to bury the 16 whales.
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