According to data obtained from SNH under Freedom of Information legislation, cull licences have been issued for some threatened species which had been “red-listed”.
The red list is compiled by bird and environmental charities, including SNH, and inclusion on the list means there is the highest level of conservation concern for that particular species.
Among the red-listed species for which licences were granted were starlings, house sparrows and grey partridges.
The vast majority of licences were issued to protect crops or livestock, or for reasons of public health and safety including the prevention of birds striking aircraft.
Some licences limit the number of birds that can be culled, while others allow for people to kill indefinite numbers.
The largest number of licences were granted for geese species to prevent damage to crops.
SNH recently faced criticised over plans to issue licences to cull ravens to boost curlew populations.
The figures show more than 100 raven cull licences were granted in 2017 to protect damage to livestock.
Scottish Labour environment and animal welfare spokeswoman, Claudia Beamish, said: “These are deeply worrying figures.
“Sadly it is often necessary for bird populations to be controlled, but these figures show licences are being granted to kill many endangered species. That cannot be right.
“Rather than reaching for the shotgun first, organisations such as Scottish Natural Heritage should be exhausting all other options before allowing culls. Scottish Labour is urgently calling for a review of why so many of these licences have been granted and whether such measures are appropriate.”
An RSPB spokesman said: “Some of the licences that permit the killing of unlimited numbers do seem alarming. But if these apply only to small areas of land, that in itself will be a limiting factor.
“Nevertheless we are struggling to understand, for instance, what serious threat to public health is posed by the endangered swift that requires indefinite numbers of them to be killed.”
A SNH spokeswoman said: “Scottish Natural Heritage works to strike a balance between the conservation and protection of species and other public interests, including minimising damage to agriculture, and health and safety.
“We are confident that all activities carried out under these licences do not affect the conservation status of any of our native species.”
She added that the majority of bird control licences with no stated limit were for reasons of air safety to prevent aircraft bird strikes and were not classified as culls.