Police Station Safe:

Found inside the police station just left of where you entered.

Code: 208

Meiji Spa Fort Keep Hill:

Need to do exploration to unlock the area. Once the area is unlocked you will find a monument with a set of numbers behind the tombstones which are 4, 1, 9, 6, 3. The last number requires another event sequence and a boss battle to get the last number which is number 7.

Code: 41736

Stranded Farm:

There are two safes within the area, one facing south where you initially find the old key. You need this key to unlock the door on the south of this screen. You will know it is the correct room if you press the menu button and under Akane's portrait it will state the area being called Farmhouse.

The other one is in north in an area called Burned House which requires the old key to enter. The safe is up a set of ladders.

Code: 6227 for Farmhouse. 8726 for Burned House

Lighthouse:

Simply go through the events in the lighthouse. The rope leading to the very top has the vault.

Code: 8726

Akane's Inheritance:

Starting home location chest. This requires the completion of the Pizza quest in Sandy Bay where you have made your own Pizza joint from your renovated house. Sleeping on the bed located on the left side of the job counter will initiate a dream sequence and the code will be provided.

Code: 74154

Thanks to Rabbit who provided the details on how to get Akane's Inheritance. Enjoy the game how you like to play it. If there is any issues with what I have stated let me know in the comments and I will review and adjust it accordingly.

If there is future content I will update the guide whenever I can.