Animal rights campaigners have been trying to stop the SNH culling the animals.
But experts say they need to get rid of 5,000 of the creatures to protect rare wading birds on the island because the hogs are munching on their eggs.
Wildlife protection groups say the whole thing has been a waste of money. They say they have saved 140 of the animals so far and have taken them to new homes off the island.
The cull has stopped for the time being because lots of baby hedgehogs are due to be born soon.
The SNH don't want them left orphaned.
During the rest of the year, two members of the culling project will stay on the island to study the hogs, their habits, and the birds.
Then next year, the SNH will think about whether to start the cull again and extend it to neighbouring islands.