Details of the alleged crime have not been revealed but media reported the diplomat left last week with a broken nose and black eye.
Foreign Affairs Minister Murray McCully said he was disappointed at the US refusal and in response had asked for the man at the center of the police investigation to be withdrawn from New Zealand.
Police said they were called to an incident in Lower Hutt, on Wellington's outskirts, in the early hours of March 12, which "involved an individual from the US embassy in Wellington."
By the time they arrived, the person had left the scene and no arrests were made.
Attempts to further investigate hit a diplomatic brick wall.
Local media named the diplomat as Colin White and said he left Wellington with his wife and children. TVNZ reported that White was a technical attache who had been working closely with New Zealand's intelligence service, the GCSB.