The 25,000-acre nature reserve at Killarney National Park in Co Kerry and Bull Island in Dublin are among a number of bird sanctuaries to be listed as "areas of sensitivity" by the Irish Aviation Authority (IAA).
Operators of low-flying aircraft, including helicopters, will be requested in future to avoid the sites where possible because of noise and other adverse effects on the environment.
The sites will not become "no-fly zones", but will be classified "prohibited zones" in the internationally recognised pilots' and aircraft operators' handbook, the Aeronautical Information Publication (AIP).
The new advice, which will be contained under the section Bird Migration and Areas with Sensitive Fauna, will be included in the updated AIP in December.
Currently, only the North and South Slobs in Wexford harbour are designated as "sensitive" by the IAA. This is partly due to the hazards the large bird migrations may pose to craft.
Pilots are asked to avoid the North Slob between October and the end of April, for instance. However, aircraft operators' attention is drawn to large bird migration areas all around the coast.
The designation of Killarney comes after representations by conservation groups such as An Taisce and the Killarney National Park Liaison Group attached to the National Parks and Wildlife Service, which have become increasingly concerned about aircraft interference with the tranquil ethos of the park, a Unesco biosphere reserve. The prospect of low-flying commercial aircraft taking tourists to view the park and the growth of traffic into Kerry airport has led to concerns for the integrity of the park's peacefulness.
Under the new listings, pilots operating at lower altitudes are reminded of the adverse effects on the local environment, on people and property as a result of noise disturbance, according to a spokesman for the IAA.
"Pilots are requested, wherever possible, to pre-plan to avoid flying over or in close proximity to areas of sensitivity during the course of normal navigation. A local aerodrome should, on request, be able to provide a brief for pilots on areas of local sensitivity," he said.
Breaches of the guidelines will not result in penalties, but the aviation authority can contact aircraft on foot of complaints.