Pagi-pagi = in the morning ? It's not accepted but I have seen it elsewhere and google translate understands it.
I can think of examples of "in the night"
The things that go bump in the night. She was awakened at some point in the night by her recurring nightmare. .. like two ships passing in the night. During the summer, bears sometimes sleep a few hours in the night. However, we use "at night" frequently, because it refers to certain point (or interval) in time (we say, "at 3:00 pm", not "in 3:00 pm") He comes home late at night. (means perhaps at 11:00 or 12:00).
We liked to take our walks at night when it is cool. (it means usually not any time during the night, but certain hours before sleeping)