Japanese government’s interpretation of the definition of refugee status is beyond strict, to a level where it detracts from the original intention of refugee protection. この表現は自然ですか？

Yes, the comma after "strict" is necessary. The comma is there to continue the sentence. If you replace the comma with a period, the sentence is now, "Japanese government's interpretation of the definition of refugee status is beyond strict." Now the sentence is just a statement. The comma is there to continue the sentence into the description of the statement sentence. Therefore the comma is necessary.

You did very well. Good job!