The Mediterranean gull and black-headed gull eggs were illegally harvested from from islands in Poole Harbour, Dorset.
The theft has been branded "sickening" by bird charity Birds of Poole Harbour.
The group said some eggs - sometimes eaten as a delicacy - were not cleared for human consumption.
Dorset Police and Natural England have launched an investigation.
Natural England is urging any restaurants or pubs to ask to see a valid licence before buying eggs to prepare in meals.
Birds of Poole Harbour had been surveying a group of islands in the harbour when the theft was discovered.
Mediterranean gulls are classified as a Schedule One species, meaning anyone disturbing their nests must have a special licence.
Paul Morton, who runs the charity, said Mediterranean gulls' eggs were not approved for human consumption, and could be a "health issue".
"I'm distraught, really. To see the taking of hundreds and hundreds of eggs from an important colony is quite sickening," he said.
Mr Moreton said there had been previous convictions for egg poaching in the last 10 or 15 years.
He said continued monitoring was needed to understand the effect on the gull population in the harbour, which he said had fallen by 70% since 2008.
Hundreds of eggs belonging to a protected species of bird have been stolen from an important nesting site, with fears they could be sold to the restaurant industry.