Maintenance men at the Eden Project in St Austell, Cornwall, discovered the birds had pecked holes in one of the giant plastic domes which form part of the environmental project.
Recorded seagull distress calls will be played to drive the birds away from the Â£86m complex.
The domes, or "biomes", are essential to re-create climates from around the world for plants at the attraction.
The gulls are an inherent problem - they will fight themselves if they see their reflection
Paul Travers, the Eden Project
The biomes - the largest of which could house the Tower of London - are made up of thousands of three-layered plastic "pillows".
They are tough - one of the hexagons can take the weight of a rugby team - but the gulls managed to make an impression.
Punctures were discovered in the smaller warm temperate dome and the plastic layers have now been replaced.
Project director Paul Travers said: "The gulls are an inherent problem - they will fight themselves if they see their reflection.
The millionth visitor arrived in June 2001
"When they peck at their reflection in glass windows they back off - but the thousands of plastic pillows that make up the biomes are softer.
"We have three pairs of buzzards around Eden, and when they take the day off there is no one to frighten the seagulls away."
The Eden Project has become Britain's third most popular tourist attraction since it opened in March last year, attracting two million visitors.
Each biome houses thousands of different species.
Boardwalks lead visitors through 12,000 plants, taking them from the Oceanic Islands to Malaysia and from West Africa to South America.
The Eden Project calls itself "a gateway into the world of plants and people" and aims to show visitors how sustainable development depends on plants.
- Old Master
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Historical note: Eden is the second Grimshaw building to fall victim to seagulls. The first was a factory building in Warrington at the end of the 1970s. Seagull feathers and dung blocked the concealed drainage outlets on the roof, causing rainwater to build up, whereupon a corner of the roof collapsed. Clearly those birds have it in for him.
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