The authority has said chickens which are kept inside for 12 consecutive weeks or longer can no longer be identified as free-range and this must be made clear on the labels of eggs.
The change comes after the Swedish Department of Agriculture warned egg farmers to keep chickens inside due to H5N8 bird flu risk last November.
Many countries in Europe, including the UK, Denmark and Czech Republic, have been affected with bird flu over the winter months, leading to many free-range chickens being kept indoors.
The spread of bird flu has led to increased EU egg prices and a shortage of free-range eggs.
H5N8 bird flu is not harmful to humans and thus there is no danger in eating chicken or eggs.