Spring Boot 2.1.0 with Flyway 4.2.0

I had the same problem with PostgreSQL 9.2, and used the following class to solve the problem.

Be aware though that all the custom properties you might set in the Spring Boot properties will be ignored, since that replaces the whole Flyway autoconfiguration by your own. So you might have to add some additional code to fit your needs.

@Configuration
class FlywayConfig {
    @Bean
    fun flyway(dataSource: DataSource): Flyway {
        val flyway = Flyway()
        flyway.dataSource = dataSource
        return flyway
    }

    @Bean
    fun flywayInitializer(flyway: Flyway): FlywayMigrationInitializer {
        return FlywayMigrationInitializer(flyway, null)
    }

    /**
     * Additional configuration to ensure that [EntityManagerFactory] beans depend on the
     * `flywayInitializer` bean.
     */
    @Configuration
    class FlywayInitializerJpaDependencyConfiguration : EntityManagerFactoryDependsOnPostProcessor("flywayInitializer")
}

PS: this is Kotlin code, but you should be able to translate it to Java fairly easily.