We urge the US to "stop smearing the Chinese side on cybersecurity issues," China's foreign ministry said in a statement, adding that it had lodged an official protest.
China said the US should drop the prosecution "to avoid serious damage to the relations between the two countries".
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Beijing accused Washington of "blame-shifting" and of carrying out hacking attacks against other countries.
"It has long been an open secret for the relevant departments of the United States to conduct large-scale and organised network theft and monitoring and monitoring activities against foreign governments, enterprises, and individuals," said the statement, attributed to foreign ministry spokeswoman Hua Chunying.
In charging the two alleged Chinese hackers, the Justice Department said the group they work for targeted firms which help other companies manage their information technology systems -- potentially giving attackers entry into the computer networks of dozens of companies.
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Western governments, including the US allies Britain and Australia, have accused Beijing of cyber-attacks.
China described those claims as "purely made out of thin air", warning other countries to "stop deliberate defamation of China, so as not to damage... bilateral relations".
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