I manually removed all data from Google Cloud Datastore using delete button on https://console.cloud.google.com/datastore/entities/query. However, when I checked indexes they are still remaining and there is no delete button on https://console.cloud.google.com/datastore/indexes. I tried to use console command
gcloud datastore cleanup-indexes
But this command does not help.
Are there any way to clean the indexes?
You can find more details on how the workflow of Datastore indexes should work on the documentation. Specifically, there is an entry explaining how to delete unused indexes and a summary of the workflow of indexes.
In short, in order to force the deletion of indexes (because they are not automatically deleted by default, as they are kept for some time to ensure that performance is not affected), you will first have to update your local index.yaml file, deleting the indexes that you no longer need. Then, you can use the command you shared pointing to the local file, and your indexes should disappear:
gcloud datastore cleanup-indexes /path/to/file/index.yaml