US-based news site Quartz reported all Filipino press would be flying the traditional route to the summit, with a stop over in Los Angeles - the shorter route and typical transit between Manila and Peru.
Duterte has publicly expressed his distaste for the US.
Last month on a state visit to Beijing, China he announced a "separation from the United States" and questioned why Americans had such easy access to the Philippines when Filipino's were often denied visas.
Leo Lim-Herrera, an official in the Philippines foreign affairs department, told Quartz "technical matters, like the capacity of the plane and fuel storage," were the reasons Duterte was taking the unusual route to the summit.
This year's annual APEC meeting will be held from November 19-20 in Lima, Peru.