Hi,
He had applied for the passport on 04/04/06, but he hasn’t received yet.
Is this statement correct? No.
You need an object for the verb 'receive'. You don't seem to have a context that needs the Past Perfect tense. Unless you have earlier referred to this particular passport, say 'a'.
Say He applied for a passport on 04/04/06, but he hasn’t received one yet.
Best wishes, Clive