Customers can call Apple Support at 0120-27753-5 to have their devices picked up for repair, a support page on the company's Japan site says. There could be delays in pickup and delivery because of the floods.
Apple typically doesn't cover liquid damage, but made an exception following the disaster. More than 120 people were killed by floods and landslides in southwest Japan this month. Thousands of homes were damaged and several more lost power.
Apple's memo expresses sympathy for anyone affected by the floods.
Customers have until the end of September to have their devices repaired.