A U.S. Customs and Border Protection spokesman says the agent fatally shot "a suspected illegal border crosser" after the agent was assaulted.
In a short statement, spokesman Michael Friel offered no details about the nature of the assault or how the agent encountered the person at the border.
The man's nationality and name have not yet been released by authorities.
The Bellingham Herald newspaper has reported that the agent wasn't seriously hurt. Whatcom County Sheriff Bill Elfo says an agent who was also at the scene shot the man in the head.
The Canada Border Services Agency referred requests for comment to U.S. authorities and did not immediately respond to questions about whether it was involved in the investigation.
The Bellingham Herald reported that shortly before the fatal shooting, a Sumas police officer reported shots had been fired and called for backup.
The road where the shooting took place is about 300 metres from the U.S.-Canada border.
The small border crossing at Sumas is about 80 kilometres southeast of Vancouver.
— With files from The Associated Press