The find comes after an extensive probe by police in at least three countries, an investigation which had seen the arrest of a man in Finland who was caught with 10,000 rare eggs back in June.
The Swedish suspects, who are believed to have poached the eggs from bird nests around the nation, had connections with the Finnish thief as well as collectors in Britain.
“There are different forums on the internet that connect these people,” investigator Stig Anddersson told the local Härnösand Allehande newspaper.
An egg collector who was caught in Britain had even tipped off one of the Swedes in an email to alert them to the probe.
Armed with a search warrant, investigators swooped in on a house in Härnösand, on the east coast of northern Sweden, where they found over 2,000 eggs hidden under a trapdoor.
The collection included eggs from owls, eagles, chickadees, nightingales, cranes, and plovers, some of which are endangered species in Sweden.
The egg thieves are believed to harvest their collections and meet with other like-minded people to trade their eggs.
The three men now face charges of aggravated hunting crimes and breaching protected species laws.
One area from where many of the eggs are believed to have been taken is the nature reserve in Stekenjokk mountains in northern Sweden.
While stealing eggs is illegal in Sweden, police suspect the men scrambled to cover their tracks by changing the labels on their eggs to make it look like they had collected them before the practice was outlawed.