The RAF has been accused of causing the deaths of kittiwake chicks when jets flew low over their island nesting sites and scared tens of thousands of birds.
Youngsters were knocked into the sea and drowned in the mass panic which followed the training exercise over the Farne Islands off the Northumberland Coast on Tuesday.
Locals said they believed a no-fly zone over the wildlife haven was breached, and the National Trust, which manages the islands, will make an official complaint.
Andrew Douglas, who operates two visitor boats from Seahouses, was out at sea with a visitor group when the jets flew over.
He said: "The RAF went right over the top of the islands.
"You should have seen all the people's faces on the boat and seen all the birds go flying into the sky. It was not very nice.
"We have 80,000 pairs of birds here.
"The jets scared them and they knocked the chicks into the sea as they took off.
"I was under the impression there was a no-fly zone here during the breeding season.
"I don't know much about jets, but I would have thought it was really dangerous because if a plane sucked a bird into the engine it could come down."
Mr Douglas said bird numbers were down this year due to the poor weather.
Rain has flooded the puffins' burrows, killing their young.
"The birds have put up with some rubbish this year and the last thing they need is this disturbance."
The National Trust's head ranger on the Farnes, David Steel, voiced concerns on Twitter saying the RAF knew pilots were not supposed to allow jets to fly low over the islands, adding: "Another letter will be winging its way to them."
An RAF spokeswoman said: "Any complaints will be investigated thoroughly and should it be deemed that the rules have been broken, appropriate action will be taken."
Simon Lee, National Trust property manager for The Farne Islands, said: "It's true we've had a number of incidents of low flying jets across The Farne Islands. The matter is being investigated by both the RAF and the National Trust and we are both hoping for a speedy resolution imminently."