They found the virus on air particles outside barns housing infected flocks, prompting their belief the virus can be carried by winds.
But the main transmission between poultry barns is people and equipment, they say.
More than 49 million birds died or were euthanized this spring in 15 states as the virus spread from the Pacific Northwest into Midwest farms, making it the worst outbreak the U.S. has experienced.
Hard hit were turkey farms in Minnesota, the nation's leading turkey grower, and chicken farms in Iowa, the leading egg producer.
The USDA says its staff found that infected and non-infected farms shared equipment, employees moved between them, and vehicles weren't disinfected when moving between farms.
It also heard reports of rodents or small wild birds inside the poultry houses.
"We are compiling these observations and will present our findings in a subsequent update of this report.
“Until then, USDA is collaborating with affected industries and states to implement more stringent biosecurity procedures while continuing to work on identifying and mitigating other possible disease pathways in poultry farms nationwide," the report said.
As for wind, they report that preliminary analysis of wind data "shows a relationship between sustained high winds and an increase in the number of infected farms approximately five days later."
The disease appears to have been eradicated from commercial flocks in Canada. There were outbreaks in the Fraser Valley area around Christmas and three farms in Oxford County, Ont., in April.