Zheng "protested" the actions by the United States, saying the indictment had seriously harmed relations between both countries, the foreign ministry said in a statement on its website.
Zheng told Baucus that depending on the development of the situation, China "will take further action on the so-called charges by the United States".
It was the first criminal hacking charge that the United States has filed against specific foreign officials, and follows a steady increase in public criticism and private confrontation, including at a summit last year between U.S. President Barack Obama and Chinese President Xi Jinping.
The indictment is likely to further roil relations between China and the United States. Besides cyber-hacking, Washington and Beijing have grappled over a range of issues, including human rights, trade disputes and China's growing military assertiveness over seas contested with its neighbors.
"The Chinese government and military and its associated personnel have never conducted or participated in the theft of trade secrets over the Internet," the foreign ministry quoted Zheng as telling Baucus.
Zheng told Baucus that the U.S. attitude to Internet security was "overbearing and hypocritical" and urged the United States to give China a clear explanation on reports that Washington has long spied on the Chinese government, businesses, universities and individuals.
The U.S. Embassy to China spokesman, Nolan Barkhouse, confirmed the meeting but declined to provide more details.
China's Ambassador to the United States, Cui Tiankai, also "made solemn representations" to the State Department on Monday.
"The accusations that the United States have made against these Chinese officials are purely fictitious and extremely absurd," Cui was quoted as saying by the state-run China News Service said.
China's defense ministry summoned the American military attaché on Tuesday to protest what they said were actions "that seriously violated norms governing international relations and for seriously slandering the image of the Chinese army".
"DOUBLE STANDARDS"
The angry reaction from Beijing is likely to be the first major test for Baucus, who arrived in Beijing in March, as he seeks to balance U.S. interests with the desire for more economic cooperation with China.
China is the United States' biggest foreign creditor. As of February, China held $1.27 trillion in U.S. Treasury bonds, according to Treasury Department data.