The Partnership for Action Against Wildlife Crime (Paw) has issued guidance to drone users to avoid causing creatures stress.
Drones have become increasingly popular for taking aerial photographs and for conservation work, according to the group, but a licence is often required.
Scottish Natural Heritage (SNH) staged a demonstration of best practice at Battleby in Perthshire on Thursday.
Andy Turner, a wildlife crime officer at SNH, said there have been incidents of seals being disturbed at protected sites and reports of drones being used to film sea bird colonies and raptors.
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He said: "While the footage from drones in these circumstances can be very spectacular, the operator must be mindful of the effect on wildlife.
"Birds of prey in particular can see drones as a threat and act aggressively towards them, causing both injury to themselves and damage to the drone.
"We would encourage anyone wishing to film wildlife with a drone to contact SNH for advice and, if necessary, apply for a licence."
Paw said it wanted people to be clear that the law protects the nests of wild birds from any form of damage or obstruction.
Some birds and mammals, like dolphins and whales, are protected from disturbance at any time.
PC Charlie Everitt, from the UK National Wildlife Crime Unit, said: "Breeding wild birds, dolphins, whales and seals are all protected from harassment or disturbance by law that currently imposes fines up to £5,000 or imprisonment for up to six months on those who break it.
"Irrespective of whether the offender is an egg collector, boat skipper or drone operator, the possible sentences are the same.
"It is therefore essential that drone operators understand the law, research the legal status and behaviour of any wildlife they intend to film, and obtain the necessary licences to keep on the right side of the law."