I did hear rumors of Japan doing this intentionally to make it look more under control than it was.
Another possibility is that medical resources are being monopolized by covid patients, or people don't want to go to hospital for fear of catching it themselves. This situation is still caused by covid but wouldn't be shown in the reported deaths from covid.
The article brings up a valid concern, but doesn't explore any other possibile explainations which is irresponsible when people are already panicking.