Are you using the cable and the wall mounted charger that was included with your device, or are you using a different charger? How long does it approximately take to charge device from 0% to in your case 99% when it's powered off?
If you have another Xperia charger at hand you can try charging your device with that one, or if one of your friends, colleagues or family members also have an Xperia device and you can borrow their charger.
With your current charger, is there any change if you restart the device in safe mode and try charging it? This will tell us if a downloaded application is the cause of this behaviour.