In a statement Thursday, Bayer said its in-house cybersecurity team found signs of malicious software associated with the group Winnti on company systems in early 2018.
The Leverkusen-based company said there were "no signs of data outflow" and the affected IT systems have since been cleaned. It said prosecutors in nearby Cologne have opened an investigation.
German public broadcasters Bayerischer Rundfunk and NDR reported that the malicious software was previously discovered on systems belonging to steel and engineering company Thyssenkrupp in 2016.
A 2013 report by security researchers at Kaspersky Lab claimed Winnti "has Chinese origins."
German officials have in the past warned of industrial espionage from China.