The concern of the Hebridean Whale and Dolphin Trust over the effect of the twice-yearly Joint Warrior military exercise is highlighted in its latest annual report.
The UK-led land, air and sea exercise, the largest in Europe, is staged off the north-west coast each spring and autumn. It features submarine warfare and loud missile and small-arms fire.
Kerry Froud, Marine Biodiversity Officer for the trust, said yesterday: "There are different worries, including that if the sonar from the vessels is quite intense and close by it could rupture the eardrums of whales and dolphins and there could be an issue with seals too.
"Whales and dolphins use echo-location to hunt and to navigate and if the sound is interfered with it can interfere with their navigation.
"Another concern is that it could scare them away … there are eye-witness accounts of minke whales that seem to be fleeing the area."
Now the trust says it will will send its survey vessel the Silurian into the mock-war zone this autumn to monitor the effects for a ten-day survey of the Autumn 2014 Joint Warrior exercise.
A Ministry of Defence spokesman said the MOD is committed to taking all practical steps to protect the environment and mitigate effects on marine mammals.
She added: "Environmental Impact Assessments have been produced where required, such as for the use of Active Sonar and live weapons, as well as consultation with landowners, national stakeholders and local communities."