The secret doors are located in the cities of Enhasa and Kajar in the Kingdom of Zeal year 12.000(BC) ancient time. We arrive at the Kingdom of Zeal after crossing a portal when we end chapter 17: Unnatural Selection?. The secret doors can be unlocked since chapter 18: The Magic Kingdom and beforeending chapter 21: What Lies Beyond? (this chapters ends after arriving at Zeal Palace and defeating Dalton).
Secret Door Enhasa and Kajar
Secret Door Enhasa
To open the secret door you need to open this spell books in this order: Water, Wind, Fire (all located inside of Enhasa).
Once this steps are done the secret door will be open, and if you enter there will be a Nu and if you speak with it you can fight it.
A tip for this fight: once the fight starts there will be 6 of them, some of them will put you at 1 HP and the others will deal 1 damage. My team was Crono (lightning II), Marle and Frog (healing).
After you defeat them they will give you a magic capsule and a speed capsule.
Secret Door Kajar
This secret door is unlocked when you open this spell books in this order: Water, Wind, Fire (all located inside of Kajar).
Once you open the spell books a bookshelf will dissapear revealing the secret door. When you enter the door there will be a Pozoyo Doll and when you interact with it you will get a Black Gemstone/Black Rock.
If you equip this item you will be able to use Triple Tech Eternal Darkness/Dark Eternal when your team is Marle-Lucca-Magus.