It was not immediately clear how many staff were affected by the firings, which the sources said occurred overnight.
A USDA spokesperson would not comment specifically on whether people were fired, but said the department was "optimizing operations, eliminating inefficiencies, and strengthening its ability to serve farmers, ranchers, and the agriculture community."
The administration, led by Elon Musk's cost-cutting Department of Government Efficiency, has fired thousands of federal workers this week.
The affected research staff worked at the National Institute of Food and Agriculture, which supports agricultural science and technology research, and the Economic Research Service, which produces reports and data on the farm economy.
Also fired were probationary loan officers at the Farm Service Agency, which processes farm loans and administers other farm programs.
"The Agency finds, based on your performance, that you have not demonstrated that your further employment at the Agency would be in the public interest," said a letter sent to the fired employees, according to a copy seen by Reuters.
The letter said the employees have a right to file an appeal with the Merit Systems Protection Board. Trump attempted to fire the head of the board on Monday, who has sued to challenge the decision.
Agriculture Secretary Brooke Rollins said on Friday that DOGE has been operating at the agency for weeks and that she welcomes their reforms.
