U.S. Justice Department lawyers have sought out farmers who are opposed to Bayer AG’s $66 billion takeover of Monsanto Co., potentially creating a stumbling block to what would be the biggest ever merger in the global seed and crop-chemicals industry.

Farmers and agricultural advocates who attended at least three separate meetings say they were interviewed about their concerns over the deal, signaling that antitrust officials could use the conversations to stop the acquisition or pressure the companies to shed assets before winning approval for the merger. While no one interviewed said they’d been given a sense of the department’s direction,...