European antitrust regulators opened an in-depth investigation on Tuesday into Bayer’s $56 billion deal for Monsanto, a transaction that would create the world’s largest integrated pesticides and seeds company.

Bayer, a German chemicals multinational, announced last year that it planned to buy Monsanto, its American agribusiness rival, but it was only this past June that it sought approval from the European authorities. The regulators had previously indicated that they would scrutinize such a deal.

“Seeds and pesticide products are essential for farmers and ultimately consumers,” Margrethe Vestager, the commissioner in charge of European competition policy, said on Tuesday in a news release. “We need to ensure effective competition so that farmers can have access to innovative products, better quality and also purchase products at competitive prices.”

In a letter to the public, Ms. Vestager said the commission had received more than 50,000 emails and more than 5,000 letters and postcards, as well as Twitter posts, expressing concerns about the transaction.

Ms. Vestager said that many of the comments expressed concern about potential negative effects of Monsanto and Bayer products, including risks to human health, food safety and consumer protection. She said the companies would be bound by “strict rules” in place to address those issues.