This one is found late in the game (I found it after the third fight versus the Imprisoned). Gorko the Goron will be behind the temple researching the Goddess Walls, and one is nearby.
Found at the northern end of the circular room in the entrance. It is in front of the shortcut to the room you flooded multiple times.
Found in the room directly west of the large central first floor chamber. It is the same room with the large pool of water you eventually turn into a whirlpool.
Another in the portion of the area with the cursed water (the basement), follow the path past the lilypads to the tunnel. Defeat some Fire Keese to find some Blessed Butterflies nearby.
One in the area with the broken stone bridge, which is crossed only with the Clawshots, drop to the level below. Underneath one of the overpasses is the group of Blessed Butterflies.
Another near the “Inside Fire Sanctuary” Bird Statue, after you drop into the statue’s mouth, go along the path to find the butterflies.
A third one after jumping into the statue’s mouth (as mentioned above), go further along the path to the crumbling staircase. At the bottom, in an alcove, are the butterflies.
From the main deck, go into the nearby room inside the ship. Go down the stairway and, at the bottom, go left.
Another on the main deck, head to the eastern mast and Clawshot to the hidden deck of the ship. (It is opposite of the chest with the Piece of Heart).
In the forest room, near the Bird Statue.