From the hole in the tree that explodes as you collect the Red key, look towards the bush nearest from you. Run in a straight line until you hit an invisible wall. Then walk into the tree to your left to discover a secret hole.
After opening the Yellow key door, enter the corridor and open the middle portion of the wall to your rightmost. Unfortunately, there're no indications on the walls, so just keep trying to open the walls in this corridor if you're having difficulties finding this secret.
Right after the last secret you should see the Green key through a glass. To your right is a stone mask on the wall. However, if you look closely, you should see there's a switch behind it! Just use it (Lo Wang ignores the mask, so you don't need to destroy it), to make a wall beside you slide revealing the secret.
After getting the Green key, as soon as you emerge in the large room which had a Rail gun. Look for the closest pillar to your left. Around it should be a small portion that is different from the design of the rest of the pillar. Swim into it to get the secret.
In the same area as mentioned in the last Extra section, go to the back of the tree to the right of the altar (directions based on standing in front of the stone mask). The back of the tree is fake and hides a secret area with a Fortune Cookie.