You can receive fragments of ninjas in Elite instance. But it is random. For example you can't receive all ninjas this way, you can only get fragments of ninjas you met/fighted in story (and even after that it is not every single ninja).

Never mind my previous comment please.

I have mistaken Survival trial with Elite instance xD.

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Back to your question - it drop rate of ninja fragments is random. But you can do each of them only 3 times per day.