The researcher lied about her military background, the FBI says, amid a row over Chinese consulates.
The US says a Chinese scientist suspected of visa fraud and concealing ties to the military has fled to China's consulate in San Francisco.
Court filings by US prosecutors also say other Chinese researchers in the US have been arrested for visa fraud.
On Wednesday the Trump administration ordered the closure of China's mission in Houston, saying it was involved in stealing intellectual property.
The Chinese government called the move a "political provocation".
But President Donald Trump said it was "always possible" he would order the closure of more Chinese consulates.
In recent months his administration has clashed repeatedly with Beijing over trade, the coronavirus pandemic and China's imposition of a controversial new security law on Hong Kong.
What are the allegations about the San Francisco mission?
Court filings by prosecutors in a federal court in San Francisco say the defendant, named as Juan Tang, was a biology researcher at the University of California, Davis.
According to the filings, during an interview with FBI agents last month she said she had not served in the Chinese military.
However, the document says, an open-source investigation uncovered photos of her wearing military uniform and a search of her home found further evidence of her affiliation with China's People's Liberation Army (PLA).
"At some point following the search and interview of Tang on June 20, 2020, Tang went to the Chinese consulate in San Francisco, where the FBI assesses she has remained," the court filing, first reported on by the Axios news site. reads.
It adds: "As the Tang case demonstrates, the Chinese consulate in San Francisco provides a potential safe harbor for a PLA official intent on avoiding prosecution in the United States."
The prosecutors say that this is not an isolated one but "appears to be part of a program conducted by the PLA... to send military scientists to the United States on false pretenses".
China has not commented on the allegations.
What is happening at China's consulates?
The Houston consulate came under scrutiny on Tuesday when people overlooking the building's courtyard noticed several bins on fire.
Footage showed people throwing what appeared to be paper into the bins.
Emergency services were called to the building but Houston police say they were not granted access.
On Wednesday, the administration gave China 72 hours to close the consulate "to protect American intellectual property and Americans' private information".
Secretary of Mile Pompeo said: "We are setting out clear expectations for how the Chinese Communist Party is going to behave. And when they don't, we're going to take actions that protect the American people, protect... our national security, and also protect our economy and jobs."
The consulate is one of five in the US, not counting the embassy in Washington.
What is stoking tensions between China and US?
There are a number of flashpoints between Beijing and Washington currently. Some of the most serious are:
Coronavirus: President Trump has repeatedly referred to Covid-19, the first cases of which were reported in Wuhan in late 2019, as the "China virus". He has also alleged it originated from a Chinese laboratory, despite his own intelligence officers saying it "was not manmade or genetically modified". In response, Chinese officials have suggested, without evidence, that Covid-19 might have originated in the US
Trade: Mr Trump has long accused China of unfair trading practices and intellectual property theft but in Beijing there is a perception that the US is trying to curb its rise as a global economic power. The US and China have engaged in a tit-for-tat tariff war since 2018 as a result of the dispute
Hong Kong: China's imposition of a sweeping new national security law in Hong Kong in June led the US to revoke the region's preferential economic treatment. Mr Trump has also signed a law to impose sanctions on officials who cracked down on rights. Beijing has accused the US of "gross interference" in its domestic affairs, promising it would retaliate