Very early on in the story campaign, you'll get a notice that you've unlocked The Island, with the game asking you if you want to go there. Go and assign workers to various tasks, then go back to the main game and keep playing for a bit. Progress in The Island seems to be tied to in-game progress, not real time, so beat a couple of levels or so and then quit to the main menu and go to The Island.
If you waited long enough, there will be exclamation points on the map. Go to those areas and find the present, click X on it to send it to Ash in the main game. Go back to the main game and once you do, present received and achievement unlocked.
This seems to go for anything you can have workers create on The Island, and not just the secret packages you can get from the harbour. I got my achievement for a health refill.
(By the way, the health you can gain on The Island is *not* permanent upgrades. They're just useless refills. As soon as I figured that out, I took all my workers from the food factory and put them to work creating money and items instead.)