Assault ship HMS Bulwark has been deployed for the exercise
The Royal Navy has denied sonar noise from warships caused whales to strand themselves on beaches.
The service was responding to concerns from the Whale and Dolphin Conservation Society (WDCS) ahead of the start of a major military exercise.
Society officials said 43 marine mammals have died since February.
Joint Warrior, to be staged off the west coast of Scotland, will involve 36 warships and about 70 aircraft from the UK and 16 Nato countries.
Royal Navy assault ship, HMS Bulwark, Type 23 frigates, mine-hunters, two submarines and Royal Marines will take part.
Live firings at ranges and simulated bombing runs against island airports will be among the activities.
WDCS said there have been strandings of Cuvier's, pilot and Sowerby's beaked whales.
It and the Hebridean Whale and Dolphin Trust submitted a Freedom of Information request to the Ministry of Defence (MoD) in February to find out whether the first strandings of Cuvier's off the islands of Islay, Tiree and Harris coincided with the use of military sonar.
Sarah Dolman, of WDCS, said: "So far, we have received a less than satisfactory response from the MoD, which indicates that sonar-related whale deaths are not being taken seriously and does not ease our suspicions that these events were indeed associated with naval activities."
The Royal Navy told BBC Scotland that no whale strandings have been attributed to its use of sonar.
No vessels were in that area using sonar at time of the February strandings, a spokesman added.
The navy said it could not dispute sonar noise has an impact, but the service regarded itself as a world leader in using it responsibly.
Low frequency active sonar - the loudest used by the Royal Navy - will not be used outside of war-time when marine mammals were close by, the spokesman said.
He said specialists on board submarines can detect whales and dolphins using highly sensitive hydrophones.
Held twice a year, the Royal Navy and Royal Air Force-run exercise will involve the US, France, Germany, Denmark, Netherlands, New Zealand, Canada, Latvia, Poland, Spain, Belgium, Norway, Italy, Turkey, Portugal and Norway.