There are 27 towers of which 2 are extra and bugged, and 2 give you an item for a story/side-quest rather than a rune. So that leaves 23 towers that give you runes. Each weapon needs 4 runes to acquire and there are 6 weapons that are available outside of main story quests. The last rune (for the shield) is acquired via a side-quest involving the sisters who sell the shields.

Caliata: Near Rodia. You need to ferry to this tower. The fisherman in the docks area of Rodia town will give you a ticket for the ferry.

Bucalaci: Found in the northernmost region, in the east area of the Leon heights warp point. You cannot activate this owl tower as of v1.0.0 as the 4 urns you need to place on the circular points do not exist. This one houses one of the runes for the wind staff, which are 6. You only need 4 for acquiring the weapon.

Curria: Found just above Dinna mountains, and accessed via the west entrance of the lake nearby. You need to go around the area and kill the plant that goes underground to reveal an air draft that takes you to the tower.

Fauda: In the eastern area of Dinna mountains. You need to light up 3 bobo statues' braziers (in the southern part of the area near water) to spawn the platform that bridges the gap to the tower.

Lapazza: Found in the lost temple, in the south-east part of the second room. You need the artifact from completing the Kodige brothers quest and the lantern to access this tower. The lost temple is accessed via the meadows, through an opening in its southernmost area.

Paredda: Northern part of Garudo rocks. You have to place 3 owl urns on the 3 circular points to spawn the tower.

Pitrazza: In the northern area, there is a square with three triangle shaped tiles on which you need to place the urns found nearby. On v1.0.0 a clone also spawns just above the oasis

Grascia: Go south from the oasis and you will find ancient bones of a snake. Use the flute to reveal the tower. You also get access to the Jacu oasis club membership, which reduces the cost of the desert clothing to 100 coins.

Palumma: Accessed only by completing the right path through the forgotten path forest. The directions are N - W - N - W - N - N - E - E - S - E - E - N - N - W - N from the first area.

• You cannot get the last rune for the hammer from Frazza as you need the owl bomb. The hammer can break items that the owl bomb does, so this requirement is understandable :D
  
  
• One of the runes for the shield is a reward you get after completing a side-quest involving the sisters who sell the shields. The other three are in towers. You cannot get the shield either, because the NPC sister that gives the shield does not respond even with 4 runes
  
  
• Muccia forest has two towers, one when you visit via bobo forest through its east exit, and the other when you visit it via the forgotten path.
  
  
• For the Rancinu tower, you need to rotate the 6 owl statues to match the same large ones you find at the entrance of the area (in the water) before the owl village. The exact pattern of facing is: for row 1 - South East South and for row 2 - East South West