The environment department said anyone who injures, kills or disturbs Arctic Terns could face prosecution.
A spokesman said three walkers with dogs were seen "attacking" the birds with sticks and stones last weekend.
Biodiversity Officer Dr Richard Selman said: "Arctic terns will defend their nests and this can be painful."
He added: "Unfortunately, terns abandon their nests when the pressure from people or predators gets too great.
"They nest in a limited area and I hope people will respect the controls provided in order to give them the best chance of raising their young".
Arctic terns, which have the scientific name of Sterna paradisaea, have an average wingspan of 75-85cm.
The birds, which mate for life, lay one or two eggs in a small space of ground.
An attack on nesting birds in a breeding colony in the north of the Isle of Man has prompted a warning from wildlife officials.