Lu Jianwang, 61, and Chen Jinping, 59, both New York City residents, face charges of conspiring to act as agents for China and obstruction of justice.
They are expected to appear in federal court in Brooklyn on Monday.
BBC reports China has previously denied operating the stations, calling them "service centres" for nationals overseas.
Mr Lu of the Bronx and Mr Chen of Manhattan worked together to establish the first overseas police station in the United States on behalf of China's Ministry of Public Security, the US Department of Justice alleged on Monday.
