The Houston move comes in the run-up to the November U.S. presidential election, in which Trump and his Democratic rival, Joe Biden, have both tried to look tough towards China.
The Trump administration began increasing tariffs on imports from China, its largest trading partner, in 2018 as part of an ambitious plan to force Beijing to curb subsidies on state manufacturing and tough demands on U.S. companies in China.
United States prosecutors have accused the Chinese Consulate in San Francisco of harboring a scientist wanted for visa fraud.
The filings in US District Court in San Francisco said that Juan Tang, who worked at University of California, Davis, falsely claimed on her visa application that she had not served in the Chinese military.
Stilwell said that some of China's attempted scientific thefts in the United States had accelerated over the last six months, and could be related to efforts to develop a vaccine for the coronavirus - although he again presented no evidence.
Later, during an interview with Federal Bureau of Investigation agents on June 20, Tang "denied serving in the Chinese military, claimed she did not know the meaning of the insignia on her uniform, and that wearing a military uniform was required for attendance at FMMU because it was a military school".
China has not commented on the allegations.
Houston media reported that documents had been burned in a courtyard at the consulate building. Videos showed several garbage bins with flames coming out of them.
Multiple US officials also told NBC the Houston consulate has been used by the Chinese government to steal valuable medical research for a long time.
A US State Department spokesman said the closure was ordered to protect American intellectual property and Americans' private information. ► China can not threaten, bully countries: Pompeo Attacking China for its aggressive moves against its neighbours, including "instigating" a deadly confrontation with India in Ladakh, US Secretary of State Mike Pompeo has said that Beijing can not threaten countries and bully them in the Himalayas.
"The Trump Administration appears to view this latest action as political ammunition in the presidential campaign".
The crackdown appears to be part of Washington's effort to root out Chinese scientists and students from United States universities.
In response, China expelled about a dozen American correspondents with major United States outlets and asked four U.S. media organizations to submit details about their operations in China.
There are a number of flashpoints between Beijing and Washington now.
"China agrees that diplomacy is the preferred approach to resolving the issue of North Korea's denuclearization", Deputy Secretary of State Stephen Biegun said.
"We are setting out clear expectations for how the Chinese Communist Party is going to behave, and when they do not, we are going to take actions that protect the American people, protect our security, our national security, and also protect our economy and jobs".
Ties between the United States and China have worsened sharply this year over a range of issues, from Covid-19 and telecoms gear-maker Huawei to China's territorial claims in the South China Sea and its imposition of a national security law on Hong Kong.
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