An RCMP spokesman would not give more details and said the investigation is ongoing.
The Canada Border Services Agency (CBSA) confirmed a female border guard is facing serious allegations.
Jean-Pierre Fortin, the national president of the Customs and Immigration Union which represents CBSA agents, said the agent was arrested for facilitating movement of goods across the border.
"We think it's a very sad situation, even though that person still has the presumption of innocence at this time because it's still under investigation," Fortin said.
The CBSA believes the agent was working alone. The agency said it's collaborating with the RCMP on the investigation.