The development marks the latest setback for the world's largest maker of electronic components, which has come under the spotlight over labour unrest, a spate of employee suicides and the use of underage interns at its Chinese plants in recent years.
Liao Wan-cheng and Teng Chih-hsien, who were senior managers at a Foxconn procurement unit, were charged with breach of trust for accepting kickbacks from 10 suppliers in exchange for clearing quality checks and buying their equipment, prosecutors said.
The allegations surfaced after Taiwanese media reported last year that Teng had been detained by police in the southern Chinese city of Shenzhen for allegedly taking bribes from suppliers.
Foxconn said at that time it was reviewing its acquisition procedures and the integrity of managers, and that its operations in China had not been affected.
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Foxconn has said that the alleged violations were limited to the procurement of consumables and accessory equipment, and that the company alerted the authorities in both Taiwan and China following an internal audit.
The statement did not name the suppliers involved.
Foxconn, also known as Hon Hai in Taiwan, is the world's largest maker of computer components and employs about one million workers at its factories across China. It assembles products for top international brands such as Apple, Sony and Nokia.