Visitors from boats have also built bonfires and cleared vegetation on Les Minquiers - a group of islands and rocks to the south of Jersey.
The States is urging boat owners and visitors to respect Jersey's wildlife laws and the "fragile environment".
Dozens of people from France and Jersey visit the reefs each summer.
Dr Paul Chambers from the Environment Department said the reefs were "ecologically important".
The States said that between March and August the main islands were home to nesting seabirds and it was an offence to disturb them.
Then in autumn large numbers of migrating birds are dependent on the vegetation on the reefs for shelter and food.
Birds' nests have been deliberately destroyed and seals and dolphins disturbed around Jersey's offshore reefs, the States has said.