Bayer CEO, Werner Baumann has defended the multi-billion dollar deal, despite huge legal costs.
The German life sciences and pharmaceuticals group said that, following an internal review, it understood that this initiative had raised concerns and criticism.
"This is not the way Bayer seeks dialogue with society and stakeholders. We apologize for this behavior," Bayer said in a statement. It added, however, that there was no indication that compiling the lists was illegal.
French prosecutors opened an inquiry on Friday after newspaper Le Monde filed a complaint alleging that Monsanto had compiled a file of 200 names, including journalists and lawmakers, in the hope of influencing their positions on pesticides.
The French investigation is the latest fallout from Bayer's $63 billion takeover of Monsanto. It already faces potentially heavy costs from U.S. class-action lawsuits in which plaintiffs argue that its Roundup weedkiller causes cancer.
Bayer shares have shed more than 40 percent since a first adverse U.S. judgment on Roundup last August, leaving the company with a market capitalization smaller than the price it paid for Monsanto.
Shareholders delivered a rare rebuke to CEO Werner Baumann's management team at Bayer's annual general meeting last month, with a majority voting against ratifying the executive board's business conduct in 2018.
Commenting on the French allegations, Bayer said its law firm would inform all of the individuals on the Monsanto list about the information collected about them. Bayer would also "fully support" the French prosecutor's investigation.
Matthias Berninger, Bayer's new head of public and government affairs, would evaluate the matter internally and assess the behavior of people involved, both inside and outside the company.
"Our highest priority is to create transparency," Bayer said, adding that the Monsanto manager responsible for the issue had left the company soon after the takeover.
"Bayer stands for openness and fair dealings with all interest groups," it added.
"We do not tolerate unethical behavior in our company. Of course, this also applies to data protection regulations in all jurisdictions in which we operate."
Comment: Monsanto continues to be a bitter pill for Bayer. The above mentioned claim by Le Monde is quite in keeping with Monsanto's modus operandi - there is documentation showing that Monsanto has in the past taken extreme measures to bias courts, lawmakers, regulatory agencies and the public in order to continue selling its toxic products.