Provided are a method, system, and program for managing data migration from one data organization type to another. In one embodiment, a migration manager defers writing progress indicators to reduce data write operations during the migration process. In one embodiment, progress indicators are written to configuration areas of disk drives when a condition is met. One example of a condition is the expiration of a time period since the last progress indicator was written. Another example of a condition is an overlap between the destination of a unit of data being migrated and the source of the unit of data. Yet another example is an overlap between the destination of a unit of data and a portion of the data source which has been copied but a progress indicator has not yet been written covering the data source portion.