Source files not found for Kotlin convention packaging during JaCoCo report generation

When setting up JaCoCo for a Kotlin project using the Coding Conventions recommended directory structure (putting files at the root if they share the same common package), the test coverage is calculated as expected but the report does not show the source files due to the following problem:

Source file "com/example/controller/ExampleController.kt" was not found during generation of report.

Is there a way to configure JaCoCo to pick up files from the correct directory such as in this example from src/main/kotlin/controller rather than src/main/kotlin/com/example/controller by perhaps providing a package prefix?