The suspension followed a story in French newspaper Le Monde revealing that FleishmanHillard collected names for a reputational campaign.
Bayer has suspended work with external agencies amid a French government investigation into lists of opponents and supporters compiled for what Le Monde called a "media counter-offensive".
The newspaper reported on Friday that prosecutors in Paris were investigating lists developed to help the company respond to the crisis over its glyphosate-based herbicide, known by the brand name Roundup.
Glyphosate, which has been named in lawsuits as a carcinogen, was developed by Monsanto before Bayer acquired that company.
List of more than 200 people
The lists were created as part of a PR initiative to support glyphosate. They included the names of more than 200 people, including journalists, politicians and agricultural and non-profit leaders categorised by their position on Monsanto.
French law tightly regulates the creation of lists and databases of people based on their political views.
The investigation was prompted by a complaint Le Monde made on 26 April, after it saw one of its journalists’ names on a leaked FleishmanHillard list obtained by reporters covering the glyphosate PR campaign.
Le Monde broke news of the list on Friday.
In a statement, Bayer apologised for the creation of the list and said it has suspended its co-operation with the "involved external service providers".
The company said it will ask an external law firm to investigate the project and Matthias Berninger, head of public affairs and sustainability, will "evaluate the issue internally".
"We are also currently investigating further appropriate consequences both internally and with regard to external parties," the company said in a statement.
The investigation comes after it was reported this week that a US jury had ordered Bayer to pay more than $2bn in damages to a Californian couple who said Roundup was responsible for their cancers.
It is the third - and most substantial - award of damages against Bayer over Roundup in the US and there are thousands more legal cases in the pipeline. Bayer stock is down approximately 40 per cent since the group acquired Monsanto.
Bayer said the PR initiative supporting glyphosate began before it acquired Monsanto, and the manager in charge of the programme left the company shortly after the acquisition closed.
Crisis comms reaction
Commenting on the investigation, Sam Rogers, commercial director at crisis comms agency Rampart PR, said: "Bayer has tried to distance itself from the list compilation 'crisis' by suspending its relationship with FleishmannHillard [and] putting out a statement disagreeing with FH's approach to relationship-building. Having just had a $2bn ruling against them for giving people cancer, it's tempting to conclude this was more a commercial decision than a moral one."
Rogers said FleishmanHillard should brace itself for further fallout.
He added: "Perhaps Bayer is gearing up for a lawsuit against FH to recover some of that payment. If so, that will truly put FH's crisis comms skills to the test."
FleishmanHillard declined to discuss the issue, but said in a statement that it was proud of its work with Bayer and that it conducts itself "in keeping with the professional standards and established practices of our industry".
Fellow Bayer agency partner Publicis Consultants also declined to talk about the controversy, but said in a statement that between October 2016 and April 2017, it had "delivered public affairs work using public data for another PR agency".
Publicis added that it is conducting an internal audit of that work and that it operates according to the highest legal and ethical standards.
Another crisis comms expert, Jonathan Hemus, managing director of Insignia, said the evolving crisis had been compounded by the investigation into the controversial list.
He said: "This development… highlights the need for your crisis management planning to include a clear understanding of all relevant regulations and requirements ahead of time, rather than falling foul of them when the heat is on."
Hemus added: "It's a salutary reminder that dealing with journalists is challenging enough under the pressure of a crisis without making your task even harder by turning the media into an aggrieved stakeholder as well."
In addition to the French investigation, the list could prompt an inquiry in Belgium.
Philippe Lamberts, a member of the European Parliament based in Brussels who was included on the list, told Le Monde that he plans to file a complaint with a Belgian court.
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