The move follows a proclamation by President Donald Trump in May aimed at Chinese nationals suspected of having ties to the military. He said some had stolen data and intellectual property.
The state department gave no details. China has not commented.
Nearly 370,000 students from China enrolled at US universities in 2018-19.
A state department spokeswoman described those declined a visa as "high-risk graduate students and research scholars."
She said they were a "small subset" of the total number of Chinese students.
"We continue to welcome legitimate students and scholars from China who do not further the Chinese Communist Party's goals of military dominance," the spokeswoman said.
The proclamation of 29 May accused China of engaging in a "wide-ranging and heavily resourced campaign to acquire sensitive United States technologies and intellectual property" and said it was using some students "to operate as non-traditional collectors of intellectual property".
Some Chinese students in the US say they are facing increased hostility and suspicion on university campuses, and their reasons for studying being questioned.
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