In this sentence, "he" most likely refers to the doctor, so the doctor was late. 

The pronoun "he" typically refers to the subject of the sentence (the doctor) rather than the object (the nurse). Additionally, the context suggests the doctor is calling to explain or notify about his own lateness.

However, I should note that this sentence is somewhat ambiguous, and without additional context, there's a small possibility "he" could refer to someone else entirely (like a patient). But the most natural interpretation is that the doctor was late.
